Dev - #71

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HatPdotS wants to merge 193 commits into

mainfrom

Commits on May 18, 2026

alignment basically working
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ff7f0fa
merged device mixin changes from main
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f15766b

Commits on May 22, 2026

minor performance improvements
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3f5140f
minor performance improvements
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143e8c9
Merged in main
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21df417

Commits on May 28, 2026

Stable FRF
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6b0272f

Commits on Jun 1, 2026

FRF fixed and production ready.
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c439431

Commits on Jun 11, 2026

working on alignement
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9615447
Resolved merge conflicts
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d2b4d85

Commits on Jun 15, 2026

post merge
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0f8bd1f
ALignment works 70% of the time, main blocker is the rotation rescoring function
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2ec9fd6

Commits on Aug 19, 2026

Merge fix_alignment into alignment2 (alignment package only)

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7c034d8

Commits on Aug 21, 2026

Carry the derived per-atom state through Model.copy

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c284281
Fix the reciprocal-space symmetry convention in the alignment package

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18899d6
Stop molecular-replacement rotation candidates compounding onto each other

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67f06c7
Bring the alignment package back onto the current core APIs

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4ec0311
Correct the alignment package's stale docstring references

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11e1d0d
Drop the sample-list minimum clamp Phaser does not have

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26483b3
Track the alignment lab harness

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8cea183
Add the FRF configuration sweep to the lab

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133bd56
Remove the FRF's dead modules, duplicates and unread state

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9826adc
Pin the FRF's reproducibility contract

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50dbe65
Drop the alignment pipeline's write-only state and dead kwargs

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b159e81
Report arms against the shipping criterion, not just against each other

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541da9b
Fit the overall anisotropy in intensity space, not log space

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27532ad
Collapse the rotation search to (search model, reflection data, model error)

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d398660
Collapse the rotation-function engine onto its own class

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3bf5243
Record the measurements behind the rotation search's constants

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7554cad
Annotate the rotation search's return types

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9bebf1e
Add the rotation search's standing benchmark: accuracy, memory and runtime

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86cb932
Correct phaser_lmax_resolution's docstring

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c8aea57
Take the process start-up out of the benchmark's first measurement

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ae040e8
Halve the SH-Bessel expansion's m range and contract in real arithmetic

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1b9bf06
Apply the radial factor per resolution shell, not per direction

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7a43918
Run the tests on a compute node, and pin the benchmark's CPU model

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8bfcc20
Key the benchmark's comparability warning on the CPU, not the hostname

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adb9d44
Cut the SH-Bessel expansion's memory traffic: 81 s -> 9.9 s at L=100

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ba41d96
Run rigid body against a sandbox so it cannot disturb its caller
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66f126b
Fuse the Legendre recurrence with the shell accumulation, in a C++ kernel

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7663c16
Add a stage-breakdown driver, now that the expansion is not the bottleneck

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5f0a782

Commits on Aug 22, 2026

Stop the dense model transform building a grid it discards

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3b4e283
Add the measurement scripts behind the dense-calc and Wigner findings

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d611ae5
Memoise the Wigner small-d blocks

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cf2f748

Commits on Aug 23, 2026

Add the French-Wilson cost and ASU-equivalence measurements

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d1244c4
Reuse the shared primitives in the FRF and put its dtype/device under config

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411ce26

Commits on Aug 24, 2026

Run the FRF's observed-side chain once per unique reflection

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00d6548
Stop concatenating the antipodal copy in the FRF expansion

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fe53d37
Make double precision a device capability rather than a constant

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8d60e82
Add characterisation tests for fraction storage and the collection targets

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992e7a6
Make f_sol_override a pure argument and keep the batch rank

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ae39a17
Add batched per-component structure factors

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3a331e8
Add batched scaling with a per-row fraction-weighted solvent

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ddd69d2
Add scaled intensity accessors

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c6e1d3f
Add batched observation accessors to DatasetCollection

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2164229
Store populations as a shared activation plus per-timepoint branching

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8e6758d
Add the two-moment intensity target

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81af1ca
Expose the two-moment model on the difference-refine CLI, with MTZ output

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34f3ab4
Add CrystFEL hkl reading and intensity simulation

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d76da05

Commits on Aug 25, 2026

Merge pull request #69 from kmdalton/fix/rigid-body-sandbox
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d98dab9

Commits on Aug 26, 2026

Give symmetry one home: a Symmetry base under SpaceGroup

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7b19cb2
Split Model's information half into a ModelContext

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c85cb12
Make HydrogenTopology a dataclass with optional fields

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261d71b
Add a topology graph that reproduces the restraint builders

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bb171d5
Build restraints from the topology, behind an unchanged read surface

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8d008c5
Generate hydrogens by instantiating the monomer template

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3908ade

Commits on Aug 27, 2026

Weight the difference target by the activation spread, and calibrate the intensity target

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40fd12e
Keep hydrogens by default, generating the ones a file lacks

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0b51a61
Move the riding-hydrogen map into the topology package

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08d62c8
Add probes for activation-dispersion identifiability and movement recovery

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134e5f4
Let a topology be subsetted and copied

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0626d64
Cover residues that differ only by an insertion code

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cba21f9
Move the restraint orchestrator into the topology package

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bb0c42e
Fold the restraint data layer into topology and drop the package

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a9f8a37
Share one Gaussian and one sigma floor between the observables

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112c7eb
Add an observable axis to the x-ray targets, with an intensity row

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85aa181
Give the collection targets the seam the single-dataset ones have

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402645c
Drop the activation-dispersion weighting; --lambda-twin needs --two-moment

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51f83b0
Add the collection target taxonomy; replace the Rice row with ml

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8f44cb8
Fit the inter-dataset scale on the work set, normalised, with a sigma option

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89a7b29
Build the joint scale fit from the target table, and normalise it

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9a85db7
Add a node-field ADP parameter wrapper

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4bfcbd0

Commits on Aug 28, 2026

Drop the sigma-weighted data-to-data scale option

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81d088b
Add a node-field ADP representation to set_adp_mode

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a95eaa5
Add node load balancing and a node magnitude prior for the ADP field

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25dae99
Drop dead code from the topology restraint orchestrator

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26107f1
Fix the corrected DED coefficients, which were phase-blind

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4a531c8
Record mask_source in the validate-ded results

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6ac01aa
Probe whether the DED correlation can compare targets across observables

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eb925b4
Record that a reflection hold-out is the wrong domain for a local feature

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0302688
Cleaned up changelog and bumped version to 0.7.0
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09cb92f
Add an E-value convention seam and a conformance harness for it

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775576b
Aggregate the movement-recovery sweep paired, seed by seed

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f482f33
Merge branch 'dev' into difference_refine_new
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119e02f
Fixed bug were anisotropic adps were being dropped on read from newer cif files.
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58e794b
forgot two testfiles
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e1f30dc
Merge branch 'dev' into difference_refine_new
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f02525c
Merge dev into alignment2

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96b65d8
Consolidate epsilon onto SpaceGroup with a convention switch

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f477f31
Route the rotation function's E values through a convention class

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f6bd44a
Give the ML rescore the sigmas, and one normaliser instead of two

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c4f8e44
Share one wrapper rebuild between Model and ModelFT restore

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dbd8ec5
Drop the stored real-space coordinate grid

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a596ed9
Merge dev into alignment2

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77d18b8
Add a bitwise pre/post check for the dev merge

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b33e26f

Commits on Aug 29, 2026

Finish the E-value consolidation, and fix the gate that hid a break

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c9dd060
Restore state dicts on CPU and move only when asked

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de6ca16
Stop three tests assuming the default device is CPU

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14137fb
Give the rigid-body step its own loss state

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5371a48
Locate the Wilson outlier fixtures through mtz_dir

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b456373
Take the collection R-factor percentiles at the configured float dtype

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4c32466
Add an absolute Wilson normaliser, and share the resolution basis

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42b9979
Normalise the alignment path through the shared Wilson fit

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8e72ae3

Commits on Aug 30, 2026

Weight reflections by inverse variance, and stop weighting twice

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cce9d46
Measure sigma_A instead of assuming it, completing the two-part system

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2c96b80
Score orientations by weighted least squares, as an alternative to the Rice

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84e6b4e

Commits on Aug 31, 2026

Add the translation-function measurement harnesses

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0aecd13
Drop four alignment modules nothing reaches

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453f418
Remove the ML rescore and the post-placement refinement

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f777255
Add the Cholesky transform at arbitrary size

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8cf986f
Give the disorder field a displacement-mode payload

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6ac873a
Cover the node-field ADP targets in the device conformance guard

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303e09d
Merge branch 'dev' into hierarchical_disorder
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ce42a73
Give both search stages one normalisation and one weight

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6a3512f
Put each stage in one module, and take the device from config

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c1a3233
Record the alignment refactor in the changelog

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b99d877
Stop the Wilson fit chasing eleven digits, and take the default dtype

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25d6b33
Note the Wilson fit changes in the changelog

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7a0140c
Add a seed sweep for structures the panel samples too thinly

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743554c
Add the Wilson-moment and 2DQ6 discrimination diagnostics

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7fe29e9
Place every rotation candidate and take the best

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b70990b
Make the pipeline's verbosity levels mean something

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67e9c46

Commits on Sep 1, 2026

Name the node-field ADP targets so a weight can reach them

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6373e0b
Register only the ADP restraints the representation calls for

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828e12c
Persist which payload a saved disorder field carries

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cc7cb62
Rebuild the saved payload on restore, and add a flat field initialisation

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2f521b3
Give Refinement an entry point for switching the ADP representation

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a610fd7
Expose the node-field ADP modes on the refine CLI

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a6621d1
Document field_aniso and preserve together in set_adp_mode

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bfc18d7
Add a preserve ADP mode that leaves the loaded ADPs alone

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9c7b97d
Rewrite the scaling guide for the Chebyshev scale and the solvent falloff

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957fb23
Ignore .DS_Store and the scaler_investigation outputs

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3f80ff7
Merge branch 'hierarchical_disorder' into dev

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cb576d8
Report the translation correlation per candidate; keep R as the ranking key

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6413c05
Make the candidate ranking rule a parameter and measure the three

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61b297e
Rank molecular-replacement candidates by the translation likelihood

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5426c09
Fixed some dtype inconsistenices and added test guarding inconsistent dtype handlign
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46d20b3
Hold R-free to its own tolerance in the AF trajectory test

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58f3757
Merge branch 'dev' of github.com:HatPdotS/TorchRef into dev
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07f28b5
Fix the translation likelihood's variance convention

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a3a14e9
restore now lands on default or passedmdevice
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ac496d9
Take the translation likelihood's model error from the shared estimator

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7d24f68
Use the shared FFT-size, Euler and symmetry-unroll helpers

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a596173
Remeasure the candidate ranking arms after the variance fix

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6edafba

Commits on Sep 2, 2026

Judge pose recovery against Cartesian mates and check the translation

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1c4e4b4
Default the translation window to the rotation window and grid the P1 copy to it

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c551305
Score translations as a normalised covariance and pick them by likelihood

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f123175
Make the empirical sigma_A read the shape of the Wilson-curve ratio, not its level

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0085457
Suppress symmetry mates in the rotation function's peak list

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eea62f8
Replace the rotation-only figures in the pipeline's documentation

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0c78eed
Re-orient one P1 copy per candidate and build only the winner's placed model

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989c8e7
Accumulate only the upper triangle of symmetry pairs in the translation function

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ec390c0
Carry ten rotation candidates by default

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ebb9393
Made grid sizing lazy and cached
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00a3511
Merge branch 'dev' of github.com:HatPdotS/TorchRef into dev
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d0c8e7c
Merge branch 'dev' into alignment2

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5c52dca
Evaluate the P1 model directly in the translation search

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0fad03d
Justify or remove every hard-coded dtype in the alignment package

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6b410f6
Keep double precision off the compute device throughout the alignment package

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d40416d
untracked alignment lab
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2d79654
Fixed mps test failures
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0456966

Commits on Sep 3, 2026

Write our own refinement header instead of inheriting the input's

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18756ba
Loosened bessel function required accuracy in tests
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f9184d2
Merge commit 'f9184d27d07712ae16fd1ce3105b438b42821ac4' into difference_refine_new
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be8f2d6

Commits on Sep 4, 2026

Default the difference map to dark phases, and rename the map CLI

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859a265

Commits on Sep 7, 2026

Precondition the rigid-body parameters and stop co-refining the scale

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33a7d58
test: separate fixtures and share read-only functional setup
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bde818f
test: consolidate weighting contracts under their API owners
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d7eebba
test: replace target arithmetic demonstrations with kernel contracts
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7912ce1
test: consolidate reader contracts and exercise ModelFT caching
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b3f5871
test: make extended structure coverage explicit and lazy
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fb97d23
fix: respect configured dtype in loss aggregation
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cd199b4
Merge loss aggregation dtype fix from dev
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d1b4ed2

Commits on Sep 8, 2026

Commits on Sep 9, 2026

feat: make hydrogen generation opt-in with refine CLI flag
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4842557

Commits on Sep 11, 2026

Fixed hydrogen placement deferring to the monomer library
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b6ffbfa

Commits on Sep 18, 2026

Align difference refinement tests with dev conventions
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bda06b9

Commits on Sep 19, 2026

Add sigma_D difference weights, difference_sd target and maps in e/A^3

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e26303b
Merge feature/sigma-d-weights into dev

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5f32d32