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Add AO indices #100

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@mcocdawc mcocdawc commented Jan 26, 2025 •
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  • The new fragmentation code produces the exact same results as "autogen" where autogen does not fail, but does not suffer from the same bug as documented for autogen in Autogen is broken #101 . It is invariant under reordering the atoms.

  • It takes ca. 50ms on the 342 atom molecule of Minsik and Leah.¹ and is 6 times faster than autogen

  • remove known to fail test suspected_bug_in_fragmentation.py again

  • get rid of the # type: ignore[arg-type] in chemfrag.FragmentedMolecule

mcocdawc added 26 commits January 24, 2025 17:16
@mcocdawc
Implemented the chemical fragmentation based on Van der Waals radii
5d85b87 
Squashed commit of the following:

commit 2ee0b81
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 16:58:53 2025 -0500

    make the test more expressive

commit 7758a12
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 16:56:53 2025 -0500

    improved the documentation

commit 172ba79
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 15:43:31 2025 -0500

    finished tests for fragmentation

commit a37f291
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 15:40:33 2025 -0500

    import Self from typing_extensions

commit dbb4fb8
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 15:40:02 2025 -0500

    finished fragmented molecule test

commit 787b8a1
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 15:37:30 2025 -0500

    Revert "use binary set operators"

    This reverts commit 36b93e4.

commit 9eac60f
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 15:28:15 2025 -0500

    ignore OrderedSet

commit 36b93e4
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 15:05:31 2025 -0500

    use binary set operators

commit 73e85d4
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 13:59:15 2025 -0500

    added more tests

commit dda22ad
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 13:45:49 2025 -0500

    added tests for chemical fragmentation

commit 08cf11a
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 13:09:18 2025 -0500

    Fragmented molecule works

commit b086d53
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 12:58:09 2025 -0500

    cleanly get edges per fragment

commit 9b58985
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 12:47:32 2025 -0500

    revert back some of the last changes

commit d8b4cce
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 24 12:36:06 2025 -0500

    get edge idx

commit f9b9eda
Author: Oskar Weser <[email protected]>
Date:   Thu Jan 23 19:12:36 2025 -0500

    cleanup of comments

commit 2e952f6
Author: Oskar Weser <[email protected]>
Date:   Thu Jan 23 19:04:05 2025 -0500

    finished FragmentedMolecule :D

commit 9478649
Author: Oskar Weser <[email protected]>
Date:   Thu Jan 23 17:27:48 2025 -0500

    ignore ordered set from missing links in the documentation

commit ece0c97
Author: Oskar Weser <[email protected]>
Date:   Thu Jan 23 14:16:53 2025 -0500

    fixed mypy issues

commit 5f565d4
Merge: 46e86a9 b747e0c
Author: Oskar Weser <[email protected]>
Date:   Wed Jan 22 22:51:00 2025 -0500

    Merge branch 'main' of github.com:troyvvgroup/quemb into improve_fragmentation

commit 46e86a9
Author: Oskar Weser <[email protected]>
Date:   Wed Jan 22 21:19:46 2025 -0500

    construct bond dictionary once and pass it on

commit 60d06e9
Merge: c6a1d10 14d443f
Author: Oskar Weser <[email protected]>
Date:   Wed Jan 22 15:21:51 2025 -0500

    Merge branch 'graphgen_fixes' of github.com:troyvvgroup/quemb into improve_fragmentation

commit 14d443f
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 22 15:12:22 2025 -0500

    A truly inconsequential change to `euclidean_norm`.

commit c6a1d10
Author: Oskar Weser <[email protected]>
Date:   Wed Jan 22 14:59:00 2025 -0500

    get rid of hlist and add_centers in return

    this was discussed with Leah; they actually don't need it for mixed BE

commit 8a9413a
Author: Oskar Weser <[email protected]>
Date:   Wed Jan 22 10:00:45 2025 -0500

    made add_back H nicer

commit a64bf10
Author: Oskar Weser <[email protected]>
Date:   Tue Jan 21 17:40:37 2025 -0500

    ignore wrong mypy error

commit 7c0dd2a
Author: Oskar Weser <[email protected]>
Date:   Tue Jan 21 17:28:47 2025 -0500

    added merge sets

commit bbfdca4
Author: Oskar Weser <[email protected]>
Date:   Tue Jan 21 17:20:51 2025 -0500

    finished get_fs

commit 15e8156
Author: Oskar Weser <[email protected]>
Date:   Tue Jan 21 15:27:36 2025 -0500

    added get_fs function

commit 39dbd51
Author: Oskar Weser <[email protected]>
Date:   Tue Jan 21 15:09:32 2025 -0500

    keep info about centers that were removed because they are subsets

commit f3042cd
Author: Shaun Weatherly <[email protected]>
Date:   Mon Jan 20 12:48:09 2025 -0500

    Expose other keywords and update docstrings

commit 4af68ae
Author: Shaun Weatherly <[email protected]>
Date:   Mon Jan 20 12:36:14 2025 -0500

    Modify docstrings.

commit 47a1c4e
Author: Shaun Weatherly <[email protected]>
Date:   Mon Jan 20 11:51:44 2025 -0500

    Indexing fixes, optimization, and etc.

commit 1b7bd8f
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 17 19:49:20 2025 -0500

    extracting information from the fragments

commit cb7f8e7
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 17 16:41:36 2025 -0500

    removed wrong merge

commit 4664380
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 17 16:40:05 2025 -0500

    rename FragPart back to fragpart to have less changed files

    do that in another commit or at the end

commit 53d7faf
Merge: 2df5ea6 8c410c4
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 17 16:39:09 2025 -0500

    Merge branch 'main' of github.com:troyvvgroup/quemb into improve_fragmentation

commit 2df5ea6
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 17 16:32:38 2025 -0500

    updated chem frag

commit 2699304
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 17 14:21:17 2025 -0500

    removed # noqa E501 in fragmentation test

commit cfe71cf
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 17 14:18:38 2025 -0500

    follow PEP8 for class names fragpart -> FragPart

commit 78bb218
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 17 14:02:17 2025 -0500

    explicitly exclude python versions >=3.13

commit 0f00f02
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 17 13:58:33 2025 -0500

    use python 3.12 for the time being

commit e07822d
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 17 13:42:59 2025 -0500

    added intersphinx dependency for chemcoord

commit 6035f44
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 17 13:35:00 2025 -0500

    chemcoord dependency

commit 172f838
Merge: e4a7b31 af8a8cf
Author: Oskar Weser <[email protected]>
Date:   Fri Jan 17 13:31:03 2025 -0500

    Merge branch 'new_graphgen' into improve_fragmentation

commit af8a8cf
Author: Shaun Weatherly <[email protected]>
Date:   Thu Jan 16 18:28:59 2025 -0500

    Update `molbe_ppp`

commit 32a1eff
Author: Shaun Weatherly <[email protected]>
Date:   Thu Jan 16 18:25:52 2025 -0500

    Final formatting.

commit 5cc31d7
Author: Shaun Weatherly <[email protected]>
Date:   Thu Jan 16 18:24:24 2025 -0500

    Ruff fixes.

commit bbbbe9b
Author: Shaun Weatherly <[email protected]>
Date:   Thu Jan 16 18:21:05 2025 -0500

    Finish renaming `valence_basis` to `iao_valence_basis`

commit 5b2108b
Author: Shaun Weatherly <[email protected]>
Date:   Thu Jan 16 18:13:02 2025 -0500

    Rename `valence_basis` to `iao_valence_basis`

commit e07aa2d
Author: Shaun Weatherly <[email protected]>
Date:   Thu Jan 16 18:06:19 2025 -0500

    Test removing `fragment_map` from nitpick exceptions.

commit fcf5c23
Author: Shaun Weatherly <[email protected]>
Date:   Thu Jan 16 18:02:10 2025 -0500

    More strict typing for `adjacency_mat`

commit b8f1eaa
Author: Shaun Weatherly <[email protected]>
Date:   Thu Jan 16 17:56:46 2025 -0500

    Test `intersphinxlink`

commit 1eab146
Author: Shaun Weatherly <[email protected]>
Date:   Thu Jan 16 17:51:07 2025 -0500

    Formatting.

commit d9fee42
Author: Shaun Weatherly <[email protected]>
Date:   Thu Jan 16 17:20:38 2025 -0500

    Update `graphgen` docstring

commit 0fddbff
Author: Shaun Weatherly <[email protected]>
Date:   Thu Jan 16 17:19:00 2025 -0500

    Add checks for IAOs in `graphgen`

commit 5a6ec5b
Author: Shaun Weatherly <[email protected]>
Date:   Thu Jan 16 16:02:38 2025 -0500

    Add unit tests for energy comparisons across `autogen` and `graphgen`

commit 432efcc
Author: Shaun Weatherly <[email protected]>
Date:   Thu Jan 16 15:23:54 2025 -0500

    Remove defaults in `FragmentMap` init.

commit 5ebb8d4
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 15:51:52 2025 -0500

    Add `fragmentation_test` to mypy blacklist

commit c5b60d9
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 15:46:45 2025 -0500

    Ruff formatting yet again.

commit d21a66a
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 15:39:16 2025 -0500

    Add ruff exclusion rule for `fragmentation_tests`

commit 546ee00
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 15:33:07 2025 -0500

    Suppress E501 in `fragmentation_test`

commit 79a0627
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 15:28:25 2025 -0500

    Long line fix.

commit e9d5db9
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 15:25:02 2025 -0500

    Add unit tests for `autogen` and `graphgen`

commit 815f0fe
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 15:24:05 2025 -0500

    Fixes for `FragmentMap`

commit 7d4e7b5
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 12:54:12 2025 -0500

    Organize imports.

commit 98b4f72
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 12:52:34 2025 -0500

    Use `np.floating[Any]`

commit 31186f7
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 12:48:41 2025 -0500

    Remove unfinished code.

commit bfa1273
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 12:47:24 2025 -0500

    `FragmentMap` Docstring edits.

commit 083e275
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 12:43:14 2025 -0500

    Additions to `nitpick_exceptions`.

commit a4333a6
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 12:25:21 2025 -0500

    Final formatting

commit 79dce30
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 12:23:17 2025 -0500

    Fix formatting

commit f94c164
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 12:02:00 2025 -0500

    Remove unused kwargs.

commit 7a4e53d
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 11:59:27 2025 -0500

    Edits to `FragmentMap` typing.

commit 5fec9ed
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 11:31:37 2025 -0500

    New `FragmentMap` data class.

commit 24adc16
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 10:31:13 2025 -0500

    `norm`

commit 49c20d5
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 10:30:19 2025 -0500

    Unsuppress mypy warnings

commit ec70e05
Author: Shaun Weatherly <[email protected]>
Date:   Wed Jan 15 10:29:11 2025 -0500

    Add types package for `networkx`

commit cff391d
Author: Shaun Weatherly <[email protected]>
Date:   Tue Jan 14 13:32:28 2025 -0500

    Added complete docstring for `graphgen`.

commit cd77b7d
Author: Shaun Weatherly <[email protected]>
Date:   Tue Jan 14 13:09:55 2025 -0500

    Remove debug prints

commit f0fd882
Author: Shaun Weatherly <[email protected]>
Date:   Tue Jan 14 12:33:41 2025 -0500

    Suppress `mypy` for `networkx` imports.

commit 364ae2f
Author: Shaun Weatherly <[email protected]>
Date:   Tue Jan 14 12:27:24 2025 -0500

    `mypy` static typing.

commit 865b9c2
Author: Shaun Weatherly <[email protected]>
Date:   Tue Jan 14 12:18:52 2025 -0500

    Update dependencies.

commit 1f17bcd
Author: Shaun Weatherly <[email protected]>
Date:   Tue Jan 14 12:16:23 2025 -0500

    Final formatting

commit a37a0e2
Author: Shaun Weatherly <[email protected]>
Date:   Tue Jan 14 12:11:05 2025 -0500

    Formatting and removed unused code.

commit 17f1b84
Author: Shaun Weatherly <[email protected]>
Date:   Tue Jan 14 11:53:56 2025 -0500

    Ruff fixes.

commit 61907e2
Author: Shaun Weatherly <[email protected]>
Date:   Tue Jan 14 11:30:30 2025 -0500

    Fix reference to `frag_scratch` when `solver=="DMRG"`

commit cacf442
Author: Shaun Weatherly <[email protected]>
Date:   Tue Jan 14 11:29:24 2025 -0500

    Fix reference to `mf.mol` when `lo_method="pipek"`

commit 4a3a4b3
Author: Shaun Weatherly <[email protected]>
Date:   Tue Jan 14 11:28:47 2025 -0500

    Added `graphgen` fragmentation.

commit e4a7b31
Author: Oskar Weser <[email protected]>
Date:   Mon Jan 13 13:38:12 2025 -0500

    added chemical fragmentation

    - use van der Waals radii (relies on chemcoord)
    - much nicer code
@mcocdawc
finished hydrogen
7de17c9
@mcocdawc
better documentation
c5ece86
@mcocdawc
finished doc strings
9ff80f4
@mcocdawc
better names
5218531
@mcocdawc
increase radius by 20 % and freeze all datastructures
b941bf9
@mcocdawc
change van der waals scaling
ddaa97a
@mcocdawc
disable caching
b78e3bb
@mcocdawc
get rid of caching
1d8f6a0
@mcocdawc
corrected grammar
5f14dd7
@mcocdawc
unify the usage of the term "motif"
9e6e0e9
@mcocdawc
further clarification in comment
c7ebc06
@mcocdawc
added test for agreement with autogen
6d7d0fd
@mcocdawc
started AO index structure
931ee1a
@mcocdawc
represent fragments as Sequence[OrderedSet[...]]
684055a 
Instead of dictionaries from Origin to Motif indices.
This makes the code more general for the future

the tests will fail now
@mcocdawc
adjusted the tests of fragmented structure to the sequence format
d07e7c1
@mcocdawc
fix doc build problems
61d36ff
@mcocdawc
return motifs in order
f8af7a8
@mcocdawc
remove AO index stuff, comes later
a9f040c
@mcocdawc
fix missing index
ec0a8db
@mcocdawc
add back in the FragmentedMolecule
2f9898e
@mcocdawc
fix wrong link for DOC
006ad51
@mcocdawc
Merge branch 'chemical_fragmentation' into add_AO_indices
dfb1f7d
@mcocdawc
introduced SeqOverFrag and SeqOverAtom
0913da4 
Proper generic new subtypes of generics are not possible :(
python/mypy#3331
@mcocdawc
small reformatting
25f8ee8
@mcocdawc
added frag_idx_per_edge (formerly known as center :D)
3ca48da
@mcocdawc mcocdawc mentioned this pull request Jan 27, 2025
Open
mcocdawc added 30 commits January 28, 2025 16:16
@mcocdawc
put missing comment why ruamel is ignored
b3039d7
@mcocdawc
allow more fine-grained control over van der waals radii
fbba6bc
@mcocdawc
add easy manipulation of van der waals radii
cc27f59
@mcocdawc
Merge branch 'chemical_fragmentation' of github.com:troyvvgroup/quemb…
989b841 
… into chemical_fragmentation
@mcocdawc
finished van der Waals modification
fa035cd
@mcocdawc
ensure that H are not shared among motifs
e79c8ca
@mcocdawc
ignore missing link to Number
5bff0b9
@mcocdawc
fix doc
33a729b
@mcocdawc
fixed bug
6128157
@mcocdawc
finished
f823e13
@mcocdawc
Merge branch 'chemical_fragmentation' into add_AO_indices
e65ae76
@mcocdawc
Merge branch 'main' of github.com:troyvvgroup/quemb into add_AO_indices
5b271cc
@mcocdawc
renamed fragpart components to match autogen names
ead091d 
we can change both later, but at least current fragpart and autogen
should be consistent among each other
@mcocdawc
fixed typo edgsites -> edgesites
7aba4e0
@mcocdawc
fixed docstring variable names of autogen
d0e5b2c
@mcocdawc
successfully implemented restrict_key
372df57 
took far too long :-(
@mcocdawc
finished all existing variables
4d36ac3
@mcocdawc
fixed ordering for tests
a067acb
@mcocdawc
make order explicit in documentation
67f3ae5
@mcocdawc
Merge branch 'main' of github.com:troyvvgroup/quemb into add_AO_indices
b6230ab
@mcocdawc
reintroduced hlist_atom and add_center_atom to fragpart
0309794 
these are used in mixed basis set
@mcocdawc
nearly finished, but get wrong mypy errors
620cda9 
I really need a const OrderedSet
@mcocdawc
declare as ordered set instead of sequence
a7e1303
@mcocdawc
declare autogen matching types as list, not sequence
e101e30
@mcocdawc
expose chemfrag to fragpart
a102c95
@mcocdawc
added test for BE calculation
c6d3919 
it works :D
@mcocdawc
added BE3 test for chemgen as well
496d7e2
@mcocdawc
fixed doc
d07a9de
@mcocdawc
added missing reason to pytest skipif
f4754ba
@mcocdawc
actually allow BEn n > 9
8bf0018
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