Add support for MDA minimize_vectors

[PardhavMaradani]

This PR adds support for MDAnalysis minimize_vectors as described in MDA Issue #5234. MDA PR #5235 adds the backend support for this function in MDAnalysis. Thanks

[PardhavMaradani]

Hi, I am unable to figure out the build error below. Could you please help me and let me know if there is something I am missing? I was able to build this locally on my ubuntu environment, which is how I was able to run the performance tests with a working version in the referenced MDA PR #5235. Thanks

[PardhavMaradani]

Hi, I am unable to figure out the build error below.

I noticed that the 'Read the Docs' build has been failing for quite some time. The rest of the tests didn't seem to run and I see the following notice for that workflow:

Could someone with access please re-enable this for tests to run again. Thanks

[PardhavMaradani]

Here are the benchmark results comparing against mda version (serial):

Show benchmark results

(distopia) cmake-build/libdistopia$ ./bench --benchmark_filter="MinimizeVectorsBench"
2026-02-23T08:08:56+05:30
Running ./bench
Run on (8 X 4500 MHz CPU s)
CPU Caches:
  L1 Data 32 KiB (x4)
  L1 Instruction 32 KiB (x4)
  L2 Unified 256 KiB (x4)
  L3 Unified 8192 KiB (x1)
Load Average: 2.13, 0.95, 0.65
***WARNING*** CPU scaling is enabled, the benchmark real time measurements may be noisy and will incur extra overhead.
--------------------------------------------------------------------------------------------------------------------------------------
Benchmark                                                                            Time             CPU   Iterations UserCounters...
--------------------------------------------------------------------------------------------------------------------------------------
MinimizeVectorsBench<float>/MinimizeVectorsMDAOrthoFloat/10/0/0                   94.7 ns         94.7 ns      6775195 Per Vector=9.47334ns items_per_second=105.559M/s
MinimizeVectorsBench<float>/MinimizeVectorsMDAOrthoFloat/100/0/0                   963 ns          963 ns       717287 Per Vector=9.62792ns items_per_second=103.865M/s
MinimizeVectorsBench<float>/MinimizeVectorsMDAOrthoFloat/1000/0/0                 9700 ns         9700 ns        73683 Per Vector=9.69997ns items_per_second=103.093M/s
MinimizeVectorsBench<float>/MinimizeVectorsMDAOrthoFloat/10000/0/0               95353 ns        95353 ns         6963 Per Vector=9.53532ns items_per_second=104.873M/s
MinimizeVectorsBench<float>/MinimizeVectorsMDAOrthoFloat/100000/0/0             992317 ns       992301 ns          713 Per Vector=9.92301ns items_per_second=100.776M/s
MinimizeVectorsBench<float>/MinimizeVectorsMDAOrthoFloat/1000000/0/0          10042317 ns     10042286 ns           65 Per Vector=10.0423ns items_per_second=99.5789M/s
MinimizeVectorsBench<float>/MinimizeVectorsMDAOrthoFloat/10000000/0/0        108277702 ns    108274283 ns            5 Per Vector=10.8274ns items_per_second=92.358M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDAOrthoDouble/10/0/0                 91.4 ns         91.4 ns      7354795 Per Vector=9.14066ns items_per_second=109.401M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDAOrthoDouble/100/0/0                 906 ns          906 ns       770059 Per Vector=9.06389ns items_per_second=110.328M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDAOrthoDouble/1000/0/0              13134 ns        13134 ns        53279 Per Vector=13.1338ns items_per_second=76.1394M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDAOrthoDouble/10000/0/0            168584 ns       168557 ns         4142 Per Vector=16.8557ns items_per_second=59.3272M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDAOrthoDouble/100000/0/0          1778711 ns      1778314 ns          383 Per Vector=17.7831ns items_per_second=56.233M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDAOrthoDouble/1000000/0/0        18292648 ns     18290987 ns           36 Per Vector=18.291ns items_per_second=54.6717M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDAOrthoDouble/10000000/0/0      148940372 ns    148919329 ns            5 Per Vector=14.8919ns items_per_second=67.1505M/s
MinimizeVectorsBench<float>/MinimizeVectorsOrthoFloat/10/0/0                      16.3 ns         16.2 ns     43208169 Per Vector=1.62491ns items_per_second=615.418M/s
MinimizeVectorsBench<float>/MinimizeVectorsOrthoFloat/100/0/0                     86.4 ns         86.4 ns      8070018 Per Vector=864.065ps items_per_second=1.15732G/s
MinimizeVectorsBench<float>/MinimizeVectorsOrthoFloat/1000/0/0                     717 ns          717 ns       974746 Per Vector=717.257ps items_per_second=1.3942G/s
MinimizeVectorsBench<float>/MinimizeVectorsOrthoFloat/10000/0/0                   7669 ns         7668 ns        90964 Per Vector=766.842ps items_per_second=1.30405G/s
MinimizeVectorsBench<float>/MinimizeVectorsOrthoFloat/100000/0/0                 79084 ns        79082 ns         8730 Per Vector=790.822ps items_per_second=1.26451G/s
MinimizeVectorsBench<float>/MinimizeVectorsOrthoFloat/1000000/0/0              1790784 ns      1790715 ns          404 Per Vector=1.79071ns items_per_second=558.436M/s
MinimizeVectorsBench<float>/MinimizeVectorsOrthoFloat/10000000/0/0            22845507 ns     22844969 ns           29 Per Vector=2.2845ns items_per_second=437.733M/s
MinimizeVectorsBench<double>/MinimizeVectorsOrthoDouble/10/0/0                    20.7 ns         20.7 ns     35724392 Per Vector=2.07161ns items_per_second=482.716M/s
MinimizeVectorsBench<double>/MinimizeVectorsOrthoDouble/100/0/0                    131 ns          131 ns      5108576 Per Vector=1.30735ns items_per_second=764.904M/s
MinimizeVectorsBench<double>/MinimizeVectorsOrthoDouble/1000/0/0                  1251 ns         1251 ns       531390 Per Vector=1.25084ns items_per_second=799.465M/s
MinimizeVectorsBench<double>/MinimizeVectorsOrthoDouble/10000/0/0                12605 ns        12577 ns        54701 Per Vector=1.25775ns items_per_second=795.072M/s
MinimizeVectorsBench<double>/MinimizeVectorsOrthoDouble/100000/0/0              129167 ns       129166 ns         4503 Per Vector=1.29166ns items_per_second=774.2M/s
MinimizeVectorsBench<double>/MinimizeVectorsOrthoDouble/1000000/0/0            4042681 ns      4041971 ns          171 Per Vector=4.04197ns items_per_second=247.404M/s
MinimizeVectorsBench<double>/MinimizeVectorsOrthoDouble/10000000/0/0          46757814 ns     46754429 ns           14 Per Vector=4.67544ns items_per_second=213.883M/s
MinimizeVectorsBench<float>/MinimizeVectorsMDATriclinicFloat/10/0/0                407 ns          407 ns      1725397 Per Vector=40.713ns items_per_second=24.5622M/s
MinimizeVectorsBench<float>/MinimizeVectorsMDATriclinicFloat/100/0/0              4028 ns         4028 ns       172412 Per Vector=40.2762ns items_per_second=24.8286M/s
MinimizeVectorsBench<float>/MinimizeVectorsMDATriclinicFloat/1000/0/0            49541 ns        49540 ns        13663 Per Vector=49.5405ns items_per_second=20.1855M/s
MinimizeVectorsBench<float>/MinimizeVectorsMDATriclinicFloat/10000/0/0          579736 ns       579721 ns         1165 Per Vector=57.9721ns items_per_second=17.2497M/s
MinimizeVectorsBench<float>/MinimizeVectorsMDATriclinicFloat/100000/0/0        5813517 ns      5813530 ns          118 Per Vector=58.1353ns items_per_second=17.2013M/s
MinimizeVectorsBench<float>/MinimizeVectorsMDATriclinicFloat/1000000/0/0      59057284 ns     59056222 ns           11 Per Vector=59.0562ns items_per_second=16.933M/s
MinimizeVectorsBench<float>/MinimizeVectorsMDATriclinicFloat/10000000/0/0    629116040 ns    629096172 ns            1 Per Vector=62.9096ns items_per_second=15.8958M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDATriclinicDouble/10/0/0              388 ns          388 ns      1800398 Per Vector=38.7783ns items_per_second=25.7876M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDATriclinicDouble/100/0/0            3839 ns         3839 ns       182470 Per Vector=38.3903ns items_per_second=26.0482M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDATriclinicDouble/1000/0/0          51414 ns        51409 ns        13338 Per Vector=51.409ns items_per_second=19.4519M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDATriclinicDouble/10000/0/0        626206 ns       626194 ns         1096 Per Vector=62.6194ns items_per_second=15.9695M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDATriclinicDouble/100000/0/0      6303879 ns      6303962 ns          109 Per Vector=63.0396ns items_per_second=15.863M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDATriclinicDouble/1000000/0/0    64112752 ns     64112265 ns           10 Per Vector=64.1123ns items_per_second=15.5976M/s
MinimizeVectorsBench<double>/MinimizeVectorsMDATriclinicDouble/10000000/0/0  717845553 ns    717796220 ns            1 Per Vector=71.7796ns items_per_second=13.9315M/s
MinimizeVectorsBench<float>/MinimizeVectorsTriclinicFloat/10/0/0                   129 ns          129 ns      5393738 Per Vector=12.9301ns items_per_second=77.3392M/s
MinimizeVectorsBench<float>/MinimizeVectorsTriclinicFloat/100/0/0                  796 ns          796 ns       871357 Per Vector=7.96363ns items_per_second=125.571M/s
MinimizeVectorsBench<float>/MinimizeVectorsTriclinicFloat/1000/0/0                7579 ns         7578 ns        92136 Per Vector=7.57812ns items_per_second=131.959M/s
MinimizeVectorsBench<float>/MinimizeVectorsTriclinicFloat/10000/0/0              75614 ns        75612 ns         9297 Per Vector=7.56123ns items_per_second=132.254M/s
MinimizeVectorsBench<float>/MinimizeVectorsTriclinicFloat/100000/0/0            816490 ns       816429 ns          918 Per Vector=8.16429ns items_per_second=122.485M/s
MinimizeVectorsBench<float>/MinimizeVectorsTriclinicFloat/1000000/0/0          7795943 ns      7795841 ns           87 Per Vector=7.79584ns items_per_second=128.274M/s
MinimizeVectorsBench<float>/MinimizeVectorsTriclinicFloat/10000000/0/0        82889566 ns     82888874 ns            8 Per Vector=8.28889ns items_per_second=120.643M/s
MinimizeVectorsBench<double>/MinimizeVectorsTriclinicDouble/10/0/0                 188 ns          188 ns      3713353 Per Vector=18.8489ns items_per_second=53.0534M/s
MinimizeVectorsBench<double>/MinimizeVectorsTriclinicDouble/100/0/0               1530 ns         1530 ns       456905 Per Vector=15.2972ns items_per_second=65.3715M/s
MinimizeVectorsBench<double>/MinimizeVectorsTriclinicDouble/1000/0/0             14748 ns        14748 ns        45064 Per Vector=14.7481ns items_per_second=67.8053M/s
MinimizeVectorsBench<double>/MinimizeVectorsTriclinicDouble/10000/0/0           149509 ns       149511 ns         4580 Per Vector=14.9511ns items_per_second=66.8847M/s
MinimizeVectorsBench<double>/MinimizeVectorsTriclinicDouble/100000/0/0         1502468 ns      1502380 ns          470 Per Vector=15.0238ns items_per_second=66.5611M/s
MinimizeVectorsBench<double>/MinimizeVectorsTriclinicDouble/1000000/0/0       15557782 ns     15557979 ns           44 Per Vector=15.558ns items_per_second=64.2757M/s
MinimizeVectorsBench<double>/MinimizeVectorsTriclinicDouble/10000000/0/0     183798640 ns    183800616 ns            3 Per Vector=18.3801ns items_per_second=54.4068M/s
(distopia) cmake-build/libdistopia$ 

MDAnalysis's own asv benchmark results comparing against different backends (including this version of distopia) can be found in this comment of MDAnalysis/mdanalysis#5235. Thanks