refactor(model): Standardize Potentials to `dreid-kernel` Format by TKanX · Pull Request #16 · caltechmsc/dreid-forge

TKanX · 2026-02-17T00:22:07Z

Summary:

Refactored the model::topology module to align potential energy structures with the dreid-kernel library's API. All potential types (BondPotential, AnglePotential, etc.) now store precomputed, kernel-ready parameters (e.g., k_half, cos_n_phi0) instead of raw physical constants. This eliminates redundant computations during energy evaluation and standardizes the interface between the parameter generation layer and future simulation kernels.

Changes:

Integrated dreid-kernel:
- Added dreid-kernel v0.4.1 dependency.
- Updated paramgen.rs to use dreid-kernel's precompute() functions for converting physical constants (from TOML) into optimized kernel parameters.
Standardized Potential Structs:
- Bond: Updated Harmonic to store k_half and r0. Updated Morse to store de, alpha, r0.
- Angle: Introduced CosineLinear for 180° angles. Updated CosineHarmonic to store c_half and cos0. Updated ThetaHarmonic to store k_half and theta0.
- Torsion: Renamed DihedralPotential to TorsionPotential. Now stores v_half, n, cos_n_phi0, and sin_n_phi0.
- Inversion: Renamed ImproperPotential to InversionPotential. Now stores c_half (and cos_psi0 for Umbrella).
- VdW: Renamed Exponential6 to Buckingham. Now stores r_max_sq and two_e_max for proper energy reflection handling.
- H-Bond: Updated HBondPotential to store d_hb and r_hb_sq.
Refactored Topology Model:
- Updated Potentials struct fields: dihedrals → torsions, impropers → inversions.
- Updated IntermediateSystem to match the new nomenclature (IntermediateTorsion, IntermediateInversion).
Updated Parameter Generation:
- Rewrote generate_parameters in paramgen.rs to utilize the new precomputation logic.
- Implemented 1/3 scaling for planar inversion force constants directly during generation.
- Updated H-bond generation to use precomputed squared distances.
Testing:
- Added comprehensive unit tests for potential struct construction, equality, and cloning.
- Updated paramgen tests to verify correct precomputed values against physical expectations.

…sts with construction and equality checks

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… kernel API

…aming for consistency

… use 'atoms' tuple

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…propers' with 'torsions' and 'inversions'

…opers' with 'torsions' and 'inversions'

…s' with 'torsions' and 'inversions'

…putation

…es and refined assertions

…tial with TorsionPotential and ImproperPotential with InversionPotential

…tial type standardization

…tial type

… align with standardization

…ation

…uckingham type

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…el and rename terms

…e default function

… types

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Copilot

Pull request overview

This PR refactors the model::topology module to standardize potential energy structures with the dreid-kernel library's API. All potential types now store precomputed, kernel-ready parameters instead of raw physical constants, eliminating redundant computations during energy evaluation and providing a clean interface for future simulation kernels.

Changes:

Integrated dreid-kernel v0.4.1 for precomputing optimized potential parameters from physical constants
Renamed and restructured all potential types: DihedralPotential → TorsionPotential, ImproperPotential → InversionPotential, Exponential6 → Buckingham
Updated all potential structs to store precomputed values (e.g., k_half, cos_n_phi0, r_hb_sq) and consolidated atom indices into tuples
Added CosineLinear angle potential variant for 180° equilibrium angles
Updated default parameters TOML to explicitly include vdw_zeta for all atom types (removing the default value function)
Comprehensive test coverage for all new structures and precomputation logic

Reviewed changes

Copilot reviewed 15 out of 20 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
`src/model/topology.rs`	Refactored potential enums/structs with precomputed parameters; renamed `DihedralPotential`→`TorsionPotential`, `ImproperPotential`→`InversionPotential`; added comprehensive unit tests
`src/forge/paramgen.rs`	Integrated dreid-kernel precompute functions; updated all parameter generation to use kernel API; added extensive test coverage
`src/forge/intermediate.rs`	Renamed `IntermediateDihedral`→`IntermediateTorsion`, `IntermediateImproper`→`IntermediateInversion`; updated field names to match dreid-typer v0.5.0
`src/forge/typer.rs`	Updated topology application to use renamed torsion/inversion structures and new field names from dreid-typer
`src/forge/params.rs`	Changed `TorsionParams.periodicity` from `i32` to `u8`; removed `default_vdw_zeta()` function; clarified documentation
`src/forge/config/potential.rs`	Renamed `AnglePotentialType`: `CosineHarmonic`→`Cosine`, `ThetaHarmonic`→`Theta`; `VdwPotentialType`: `Exponential6`→`Buckingham`; updated default to `Cosine`
`src/forge/config/mod.rs`	Updated default config to use `AnglePotentialType::Cosine` instead of `ThetaHarmonic`
`src/forge/mod.rs`	Updated integration tests to use renamed potential collections (`torsions`, `inversions`)
`src/lib.rs`	Updated public API exports and documentation to reflect renamed types and new nomenclature
`src/bin/dforge/cli.rs`	Updated CLI enums and defaults; changed default angle potential argument to "cosine"
`src/bin/dforge/util/convert.rs`	Updated CLI→config type conversions for renamed angle and VdW potential types
`src/bin/dforge/commands/chem.rs`	Updated display strings for new angle potential type names
`src/bin/dforge/commands/bio.rs`	Updated display strings for new angle potential type names
`src/bin/dforge/display/tables.rs`	Updated parameter table labels: "Dihedrals"→"Torsions", "Impropers"→"Inversions"
`resources/default.params.toml`	Version bump to 1.1.0; added explicit `vdw_zeta` values for all atom types; minor parameter value updates
`Cargo.toml`	Added `dreid-kernel = "0.4.1"`; updated `dreid-typer` to "0.5.0"; fixed typo "chemoinformatics"→"cheminformatics"
`README.md`	Updated documentation to reflect new terminology and added dreid-kernel to dependency table
`MANUAL.md`	Updated CLI documentation with new angle potential default and simplified option descriptions
`ARCHITECTURE.md`	Comprehensive documentation updates throughout; added dreid-kernel integration details; updated all diagrams and tables

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TKanX added 30 commits February 12, 2026 14:19

fix(model): Standardize potential parameter names

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test(model): Enhance bond, angle, dihedral, and improper potential te…

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…sts with construction and equality checks

chore(package): Add dreid-kernel dependency

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fix(package): Correct typo in keywords from "chemoinformatics" to "ch…

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…eminformatics"

refactor(forge): Standardize angle potential names for consistency

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test(forge): Correct default angle potential type in tests to align w…

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…ith implementation

refactor(forge): Update default angle potential type to Cosine for co…

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…nsistency

refactor(cli): Standardize angle potential default value to cosine

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refactor(cli): Standardize angle potential naming to align with Dreid…

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… kernel API

refactor(model): Standardize potential function types and parameter n…

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…aming for consistency

test(model): Add unit test for CosineLinear angle potential construction

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test(model): Standardize bond and angle potential parameter naming to…

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… use 'atoms' tuple

refactor(forge): Standardize Buckingham potential naming in VdwPotent…

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…ialType

refactor(forge): Standardize intermediate angle and dihedral terminology

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test(forge): Standardize terminology by replacing 'dihedrals' and 'im…

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…propers' with 'torsions' and 'inversions'

refactor(forge): Standardize typer by replacing 'dihedrals' and 'impr…

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…opers' with 'torsions' and 'inversions'

test(forge): Standardize typer by replacing 'dihedrals' and 'improper…

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…s' with 'torsions' and 'inversions'

refactor(forge): Change periodicity type from i32 to u8 in TorsionParams

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refactor(forge): Optimize DREIDING force field potentials with precom…

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…putation

test(forge): Update parameter generation tests with new potential typ…

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…es and refined assertions

test(forge): Rename potential types in tests

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refactor(lib): Standardize potential types by replacing DihedralPoten…

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…tial with TorsionPotential and ImproperPotential with InversionPotential

docs(lib): Update parameter generation documentation to reflect poten…

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…tial type standardization

refactor(cli): Update VdwPotential conversion to use Buckingham poten…

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…tial type

refactor(cli): Rename potential types in print_parameters function to…

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… align with standardization

chore(package): Update dreid-typer dependency to version 0.5.0

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docs(readme): Add dreid-kernel crate to the list of specialized crates

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docs(readme): Standardize potential parameter terminology in document…

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…ation

docs(readme): Update van der Waals potential description to specify B…

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…uckingham type

refactor(model): Standardize angle potential parameter names for clarity

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TKanX added 8 commits February 15, 2026 16:51

docs(forge): Clarify inversion force constant terminology and update …

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…torsion comment

docs(architecture): Updates architecture docs to integrate dreid-kern…

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…el and rename terms

chore(package): Update dreid-kernel to version 0.4.1

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chore(params): Update DREIDING force field parameters to version 1.1.0

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refactor(forge): Standardize vdw_zeta parameter description and remov…

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…e default function

fix(forge): Improve error message for default parameters parsing failure

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docs(lib): Clarify descriptions for angle and van der Waals potential…

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… types

docs(cli): Standardize potential parameter descriptions and update de…

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…faults

TKanX self-assigned this Feb 17, 2026

Copilot AI review requested due to automatic review settings February 17, 2026 00:22

TKanX added documentation 📖 Improvements or additions to documentation enhancement ✨ New feature or request labels Feb 17, 2026

TKanX linked an issue Feb 17, 2026 that may be closed by this pull request

Standardize Potential Parameters to Align with dreid-kernel API Contract #15

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Copilot started reviewing on behalf of TKanX February 17, 2026 00:22 View session

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TKanX merged commit 65ee581 into main Feb 17, 2026
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TKanX deleted the feature/15-standardize-potential-parameters-to-align-with-dreid-kernel-api-contract branch February 17, 2026 00:37

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refactor(model): Standardize Potentials to `dreid-kernel` Format#16

refactor(model): Standardize Potentials to `dreid-kernel` Format#16
TKanX merged 38 commits intomainfrom
feature/15-standardize-potential-parameters-to-align-with-dreid-kernel-api-contract

TKanX commented Feb 17, 2026

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TKanX commented Feb 17, 2026

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