Update NCDF Reader to read .ncrst Restart Files #5031

jeremyleung521 · 2025-04-17T14:50:01Z

Changes made in this Pull Request:

Updated NCDF Reader to read Amber .ncrst restart files
Added tests to verify that the ncrst file is readed correctly. The test file I used is created from a .nc file already present in MDAnalysisTest
Noticed @jpkrowe did not add himself to the changelog, so also added him here.

PR Checklist

Issue raised/referenced?
Tests updated/added?
Documentation updated/added?
package/CHANGELOG file updated?
Is your name in package/AUTHORS? (If it is not, add it!)

Developers Certificate of Origin

I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.

📚 Documentation preview 📚: https://mdanalysis--5031.org.readthedocs.build/en/5031/

github-actions

Hello there first time contributor! Welcome to the MDAnalysis community! We ask that all contributors abide by our Code of Conduct and that first time contributors introduce themselves on GitHub Discussions so we can get to know you. You can learn more about participating here. Please also add yourself to package/AUTHORS as part of this PR.

…-reader

…nto ncrst-reader

This reverts commit 2ab9fe1.

This reverts commit 5bf1ce0.

jeremyleung521 · 2025-05-27T19:30:48Z

Turning this PR into a draft for now, because there is a wide-affecting bug with the SingleFrameReaderBase's n_atoms attribute, which is causing things to fail. (#5052) Will wait for that to fix itself before moving forward, as that needs to be fixed for this to be implemented properly.

orbeckst · 2025-06-12T16:13:09Z

Now that #5052 has been fixed, would it be worthwhile to rebase the PR and see if can continue?

…crst-reader

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jeremyleung521 · 2025-06-26T23:10:55Z

Regarding the status of this PR:

The MDAnalysis building failure and the n_atoms variable are both fixed. Those commits are merged in.
The main code should be done, the old tests from [WIP] Add NCRestart reader #3942 is ported as well
I need to fix/re-integrate the tests in test_netcdf.py I wrote for the previous code back into the newer version. Will do this in the next couple weeks.
All tests currently passes

yuxuanzhuang · 2025-07-13T07:07:01Z

package/MDAnalysis/coordinates/__init__.py

   +---------------+-----------+-------+------------------------------------------------------+
   | AMBER         | ncdf, nc  |  r/w  | binary (NetCDF) trajectories are fully supported with|
   |               |           |       | optional `netcdf4-python`_ module (coordinates and   |
   |               |           |       | velocities). Module :mod:`MDAnalysis.coordinates.TRJ`|
   +---------------+-----------+-------+------------------------------------------------------+
+   | AMBER         | ncrst,    |  r    | binary (NetCDF) restart file                         |
+   |               | ncrestrt, |       | Module :mod:`MDAnalysis.coordinates.INPCRD           |


yuxuanzhuang · 2025-07-13T07:09:19Z

package/MDAnalysis/coordinates/INPCRD.py

+.. Links
+
+.. _AMBER: http://ambermd.org
+.. _AMBER INPCRD FORMAT: http://ambermd.org/formats.html#restart


this link is 404 when I accessed it, maybe this one?

https://ambermd.org/FileFormats.php#restart

yuxuanzhuang · 2025-07-13T07:09:47Z

package/MDAnalysis/coordinates/INPCRD.py

@@ -22,29 +22,92 @@
 #


-"""INPCRD structure files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD`
+"""AMBER restart files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD`


Suggested change

"""AMBER restart files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD`

"""AMBER coordinate/restart files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD`

yuxuanzhuang · 2025-07-13T07:14:42Z

package/MDAnalysis/coordinates/INPCRD.py

+
+    See Also
+    --------
+    :class:`NCDFReader`


Some hyperlinks to classes within this module are not working. You need to use absolute references, for example,

:mod:`MDAnalysis.coordinates.INPCRD`

yuxuanzhuang · 2025-07-13T07:16:43Z

package/MDAnalysis/coordinates/TRJ.py

-            errmsg = (f"NCDF trajectory {self.filename} does not contain "
-                      f"frame information")
-            raise ValueError(errmsg) from None
+        # try:


Please clean up the commented-out code or add a comment explaining why it’s being retained.

…-reader

orbeckst · 2025-07-22T20:46:58Z

package/MDAnalysis/coordinates/INPCRD.py

@@ -102,7 +102,7 @@ class INPReader(base.SingleFrameReaderBase):
    * Box information is not read (or checked for).
    * Velocities are currently *not supported*.

-    .. versionchanged: 0.20.0


Why was this changed?

If you have a new change, add a versionchanged BELOW with a summary of user-relevant changes.

That was from a commit from #3942 when @IAlibay was implementing this (which I git cherry-picked). That PR never got merged/completed. I assume it's because 0.20.0 was the newest version back when this was written. I'm simply reusing some of the docstrings he wrote back then for if/when this is finally merged into develop.
https://github.com/MDAnalysis/mdanalysis/pull/3942/files#diff-866fcc034359780910de97ee91a381661555985d630bfe9d34600f254bc1bb2fR105
(Line 105 in INPCRD.py)

If you check the current develop branch, that versionchanged text isn't there.
https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/coordinates/INPCRD.py#L45

orbeckst · 2025-07-22T22:06:20Z

Ok, thanks for the explanation.

IAlibay and others added 24 commits September 2, 2018 15:16

Adds basic framework for reading NCRST files

6a75d39

Removing unused imports

5a88100

Major updates to NCRST reader

8b7dbd5

Try/except instead of it statements + docstring changes

0c457ce

64 bit offset check

d245e33

Merge branch 'develop' into NCrestart

33cbe3e

Need to check things

b420032

Merge branch 'develop' into NCrestart

08bb2b1

Some changes

7676741

Merge branch 'develop' into NCrestart

a382762

Exception + Minor docs update

df24168

More exceptions + start on tests

93f2edb

More inpcrd changes and tests

78e92d0

Error type change

474ab59

Changes to match initial PR 2326

e5d7cb6

Merge branch 'develop' into NCrestart

cee802c

Swapping to ValueErrors

2554ff0

Update _verify_units and typos

8cc8161

Merge branch 'develop' into NCrestart

5277cd0

Merge branch 'MDAnalysis:develop' into NCrestart

f9d2ab5

Update INPCRD.py

bcc58c8

working commit

30a2b12

test for NCRST

e2e0455

changelog + authors

d6627c7

github-actions bot reviewed Apr 17, 2025

View reviewed changes

jeremyleung521 added 2 commits April 17, 2025 10:52

Merge branch 'develop' of github.com:mdanalysis/mdanalysis into ncrst…

c5988e6

…-reader

lint test_netcdf.py

fb0d2e9

jeremyleung521 mentioned this pull request Apr 17, 2025

Support for Amber NetCDF Restart Files (.ncrst) #5030

Open

jeremyleung521 added 2 commits April 17, 2025 11:11

small code cleanup of TRJ.py

0f27fc4

small formatting in CHANGELOG

eb83b42

jeremyleung521 added 10 commits May 22, 2025 15:41

Merge branch 'develop' of github.com:mdanalysis/mdanalysis into ncrst…

50eb893

…-reader

Merge branch 'pr/3942' into ncrst-reader

abfb5a7

working, failing ExceptionWarning Tests

d98ebab

cleanup

37b7e1e

make NCRST work

736db88

typo in SingleFrameReaderBase

2ab9fe1

Merge branch 'ncrst-reader' of github.com:jeremyleung521/MDAnalysis i…

14daa07

…nto ncrst-reader

Revert "typo in SingleFrameReaderBase"

5bf1ce0

This reverts commit 2ab9fe1.

black lint

614f9f6

Reapply "typo in SingleFrameReaderBase"

bf68954

This reverts commit 5bf1ce0.

jeremyleung521 mentioned this pull request May 27, 2025

Fixing Typo in SingleBaseReaderClass leads to lammps test errors/failure #5052

Closed

jeremyleung521 marked this pull request as draft May 27, 2025 19:17

black lint

264215f

jeremyleung521 added 4 commits June 12, 2025 12:31

Merge branch 'develop' of github.com:jeremyleung521/MDAnalysis into n…

01234f1

…crst-reader

fix tests

6613a27

Merge branch 'develop' of github.com:mdanalysis/mdanalysis into ncrst…

4dcbf2f

…-reader

fix docstring

eca17ab

yuxuanzhuang requested changes Jul 13, 2025

View reviewed changes

jeremyleung521 added 6 commits July 22, 2025 14:33

Merge branch 'develop' of github.com:mdanalysis/mdanalysis into ncrst…

aac6b8a

…-reader

typo and doc-links fix

b44df73

doc update

32848f4

n_frames now read during init

9262e75

update tests

ec8fd95

lint for test_netcdf.py

444ece0

orbeckst reviewed Jul 22, 2025

View reviewed changes

jeremyleung521 marked this pull request as ready for review July 22, 2025 21:21

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	\| \| ncrestrt, \| \| Module :mod:`MDAnalysis.coordinates.INPCRD \|
	\| \| ncrestrt, \| \| Module :mod:`MDAnalysis.coordinates.INPCRD` \|

	"""AMBER restart files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD`
	"""AMBER coordinate/restart files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD`

Update NCDF Reader to read .ncrst Restart Files #5031

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