Eliminate size_of_val == 0 for DSTs with Non-zero-sized Prefix via NUW and Assume

https://github.com/rust-lang/rust/pull/152843

Summary:

Problem:

size_of_val(p) == 0 fails to optimize away for DST types that have a statically-known non-zero-sized prefix:

pub struct Foo<T: ?Sized>(pub [u32; 3], pub T);

pub fn demo(p: &Foo<dyn std::fmt::Debug>) -> bool {
    std::mem::size_of_val(p) == 0  // always false, but LLVM can't prove it
}

Foo has a 12-byte prefix, so its total size is always ≥ 12. Yet the comparison persists as a runtime computation in LLVM IR. This matters because Box<dyn T> drop emits this exact check to guard the deallocation call — for types with a guaranteed non-zero prefix, the branch should vanish but doesn’t.

The slice tail variant Foo<[i32]> already optimized correctly; Foo<dyn Trait> and Foo<[u8]> did not.

Root Cause:

In size_and_align_of_dst (the ADT/Tuple branch), the size computation is:

full_size = (offset + unsized_size + (align-1)) & -align

LLVM cannot prove full_size > 0 because:

1. offset + unsized_size used plain add — no NUW flag, so LLVM cannot conclude the result is ≥ offset.
2. (x + addend) & -align — LLVM has no information that alignment rounding never reduces the value below x.

Additionally, the vtable alignment range metadata was [1, u64::MAX] (only non-zero), despite the actual bound being [1, 1 << (ptr_width - 1)] (all alignments are powers of two with a tighter upper bound).

Fixed Compiler Code Generation Bugs (ICE): https://github.com/rust-lang/rust/issues/152340

[ICE]: Unexpected def_kind in codegen_fn_attrs: Const

Summary:

Problem:

Coercing a #[target_feature] const fn to a function pointer inside a const body triggers an ICE (debug builds only):

#[target_feature(enable = "sse2")]
const fn with_target_feature() {}

const X: () = unsafe {
    let _: unsafe fn() = with_target_feature; // ICE
};

assertion failed: def_kind.has_codegen_attrs()
unexpected `def_kind` in `codegen_fn_attrs`: Const

Root Cause:

Introduced in rust-lang/rust#135504 (2025-01-14, commit 8fee6a77394). adjust_target_feature_sig unconditionally calls codegen_fn_attrs(caller) to get the caller’s target features. codegen_fn_attrs requires that the DefId satisfies has_codegen_attrs(). DefKind::Const, AssocConst, and InlineConst do not — they have no codegen attributes by design. The debug assertion fires.

In release builds the call “worked” accidentally: codegen_fn_attrs on a const would reach the query machinery and happen to return empty attributes, producing a correct (but unguaranteed) result. The bug was latent until debug builds exposed it.

Solution:

Replace codegen_fn_attrs(caller) with body_codegen_attrs(caller). body_codegen_attrs exists precisely for this case: it delegates to codegen_fn_attrs for function-like DefKinds and returns CodegenFnAttrs::EMPTY for const items. A const body has no target features, so returning empty is semantically correct.

Also fix the pre-existing variable name callee_features → caller_features (the variable holds the caller‘s features, not the callee’s).

Implement Context-Aware Histidine Protonation and Refine pH Handling

Summary:

Significantly enhances the hydrogenation pipeline (ops::hydro) by introducing context-aware histidine protonation logic. It now detects potential salt bridges between histidine residues and nearby carboxylate groups (ASP⁻, GLU⁻, C-terminal COO⁻), automatically converting them to the doubly protonated HIP state when geometrically favorable. Additionally, the pH handling logic has been refined to allow users to opt-out of automatic protonation state changes by omitting the --ph flag, preserving original residue names while still adding hydrogens.

Changes:

PR: https://github.com/TKanX/bio-forge/pull/38

SEE PR #36: https://github.com/TKanX/bio-forge/pull/36

Summary:

Addresses geometric artifacts observed in reconstructed terminal atoms (N-terminal hydrogens, C-terminal OXT, and nucleic acid termini). The previous implementation of calculate_transform was too simplistic for single/double atom alignments and relied on global SVD coupling which could distort local geometry. Additionally, terminal atom construction has been rewritten to use robust local coordinate frames based on standard bond lengths and angles, rather than rough vector approximations.

v0.1.0

🚀 Features

1. Comprehensive Force Field Support

   • Extensive Coverage: Provides atomic partial charges for Proteins (29 residues), Nucleic Acids (DNA/RNA), Water (5 models), and Ions (66 types).
   • Multi-Scheme Compatibility: Supports major force fields including AMBER (ff99SB, ff14SB, ff19SB, ff03) and CHARMM (C22, C27, C36, C36m).
   • Terminal Awareness: Correctly handles N-/C-terminal protein residues (including protonation states) and 5’/3’-terminal nucleic acids.

2. High-Performance Architecture

   • O(1) Lookups: Utilizes Perfect Hash Functions (PHF) for constant-time charge retrieval, eliminating runtime hash map overhead.
   • Zero Allocation: Designed for stack-only usage with no dynamic memory allocation, ideal for high-throughput simulations.
   • Compile-Time Generation: All data is baked into the binary from CSV sources at compile time, ensuring zero startup cost and maximum optimization.

3. Portability & Usability

   • no_std Support: Fully compatible with bare-metal, embedded, and WebAssembly (WASM) environments.
   • Type-Safe API: Leverages Rust’s strong type system with enums for Schemes and Positions to prevent invalid queries at compile time.
   • Zero Dependencies: Requires no runtime dependencies (other than the lightweight phf crate), keeping the dependency tree minimal.

New Contributors

• @TKanX Lead Developer

Full Changelog: https://github.com/TKanX/ffcharge/commits/v0.1.0

v0.3.0

🚀 Features

• Refactor for Performance, Parallelism, and WASM Compatibility - by @TKanX in https://github.com/TKanX/bio-forge/pull/18
• Randomize Orientation of Crystal Waters During Hydrogenation - by @TKanX in https://github.com/TKanX/bio-forge/pull/20
• Enhance Histidine Protonation Strategy with H-Bond Angle Checks - by @TKanX in https://github.com/TKanX/bio-forge/pull/22
• Introduce WASM Bindings and Transition to Cargo Workspace - by @TKanX in https://github.com/TKanX/bio-forge/pull/24
• Implement Modern Web Application with WASM Integration and 3D Visualization - by @TKanX in https://github.com/TKanX/bio-forge/pull/26

Full Changelog: https://github.com/TKanX/bio-forge/compare/v0.2.2...v0.3.0