pip: bump nvalchemi-toolkit-ops from 0.2.0 to 0.3.1

[dependabot]

Bumps nvalchemi-toolkit-ops from 0.2.0 to 0.3.1.

Release notes

Sourced from nvalchemi-toolkit-ops's releases.

v0.3.1 Release Notes

Breaking Changes

• Virial sign convention for DSF and LJ (#56): previous implementation used the wrong sign for DSF and LJ virials. Virials now consistently follow W = -Σ rᵢⱼ ⊗ fᵢⱼ (positive pressure produces positive virial trace). A new conventions page at docs/userguide/about/conventions.md documents the convention used throughout the library.

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Additions/New Features

• Hybrid forces mode for PME/Ewald electrostatics (#57): new forces_mode parameter ("real", "reciprocal", "full") enables ~3x speedup for force and virial prediction with geometry-dependent charges.
• Left- and right-handed lattice support in cell list neighbor search (#59 ): cell_list and batch_cell_list now correctly handle both lattice handedness via absolute value of the determinant.
• CUDA 13 support (#60, #68): compatibility fixes for CUDA 13 toolkit, updated install documentation and FAQ.

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Bug Fixes

• torch.compile correctness for PME and Ewald (#53): rewrote the warp_custom_op autograd wrapper to produce computation graphs compatible with torch.compile; added comprehensive autograd unit tests.
• PME reciprocal virial shape for single-system batches (#52): virial output now correctly returns shape (n_systems, 3, 3) even when n_systems=1, for both PyTorch and JAX bindings.
• Background energy virial correction for non-neutral Ewald/PME systems (#62): the background self-energy correction now properly contributes its virial term via the strain derivative for both PyTorch and JAX.
• Detached charges/cell in PME reciprocal virial background correction (#65): prevents incorrect gradient flow through the background correction term during backpropagation.
• retain_graph=True support in warp_custom_op backward (#64): the backward pass no longer invalidates saved tensors on the first call, enabling multiple backward passes over the same graph.
• NPT/NPH strain rate tensor (#66): drag force and cell kinetic energy now use the strain rate tensor ε̇ = ḣ h⁻¹ instead of the raw cell velocity, fixing barostat dynamics for constant-pressure simulations.

v0.3.0 Release Notes

New Features

Molecular Dynamics Integrators and Geometry Optimization (#17)

GPU-accelerated MD integrators and geometry optimization are now available:

• Velocity Verlet (NVE) — microcanonical ensemble
• Langevin dynamics (NVT) — BAOAB splitting for optimal stability
• Nosé-Hoover Chain (NVT) — deterministic thermostat
• NPT/NPH ensembles — Martyna-Tobias-Klein barostat with dynamic cell fluctuations
• Velocity rescaling — direct temperature control
• FIRE2 optimizer — adaptive timestep geometry optimization with variable cell support

All integrators support both single-system and batched computation modes.

JAX Bindings (#24)

A new nvalchemiops.jax namespace provides JAX JIT-compatible wrappers for neighbor lists, electrostatics (Ewald, PME), DFT-D3 dispersion, splines, and batch utilities. Warp kernels are exposed via warp.jax_experimental.jax_kernel.

Note: Cell list operations that require runtime-dependent array allocation are not yet JIT-compatible. JAX autograd (differentiation) support is not yet implemented.

Damped Shifted Force (DSF) Electrostatics (#21)

... (truncated)

Changelog

Sourced from nvalchemi-toolkit-ops's changelog.

Changelog

0.3.0 - 2026-XX-XX

Breaking Changes

• PyTorch is now an optional dependency: The previous PyTorch-based functionality has been moved to a separate nvalchemiops.torch namespace. See the hosted documentation for a detailed migration guide. Previous imports should still be supported, however will issue deprecation warnings. The old interfaces will be removed in an upcoming release.

Added

• Framework-agnostic Warp kernel layer for all modules (neighbors, electrostatics, dispersion, math/spline) that operates directly on warp.array objects. A best effort to have interfaces that mirror their framework bindings is made, however due to differences in functionalities this may not always be possible.
• Thin PyTorch bindings in nvalchemiops.torch.* that wrap the Warp kernels.
• Deprecation warnings for old import paths to guide migration.
• JAX bindings in nvalchemiops.jax.* that wrap the Warp kernels, providing support for neighbor lists, DFT-D3 dispersion, electrostatics (Coulomb, Ewald, PME), and splines with jax.jit compatibility.
• GPU-accelerated molecular dynamics integrators with single-system and batched modes: Velocity Verlet (NVE), Langevin (NVT), Nosé-Hoover Chain (NVT), NPT, NPH, and Velocity Rescaling
• FIRE (Fast Inertial Relaxation Engine) geometry optimizer with adaptive timestep, variable cell optimization, and cell filtering for constrained optimization
• Lennard-Jones potential with GPU-accelerated energy, force, and virial computation integrated with neighbor lists
• Batch processing utilities (nvalchemiops.batch_utils) with support for both batch_idx (ragged arrays) and atom_ptr (CSR format) including operations: batch_sum, batch_mean, batch_max, batch_min, batch_scale, batch_normalize, batch_gather, batch_scatter
• Cell manipulation utilities including volume calculation, inverse, wrapping, alignment, and transformation
• SHAKE and RATTLE constraint algorithms for bond length constraints and rigid molecules

Commits

• 8f4ab23 0.3.1 rc docs (#70)
• 4836469 CUDA 13 instructions (#68)
• 7d0b325 Update init.py
• 0144cf3 fix: use strain rate tensor in NPT/NPH drag and cell kinetic energy (#66)
• 1164fd3 fix: support retain_graph=True in warp_custom_op backward (#64)
• ec4b881 fix: detach charges and cell in PME reciprocal virial background corr… (#65)
• 687aefb fix: add background energy virial correction for non-neutral Ewald/PME system...
• 8bc0643 CUDA 13 support (#60)
• 7b55c48 update README Key Features for v0.3.0 (#45)
• bf593f5 Add testmon to CI testing (#55)
• Additional commits viewable in compare view

[github-actions]

Original Dependabot description

Bumps nvalchemi-toolkit-ops from 0.2.0 to 0.3.1.

Release notes

Sourced from nvalchemi-toolkit-ops's releases.

v0.3.0 Release Notes

New Features

Molecular Dynamics Integrators and Geometry Optimization (#17)

GPU-accelerated MD integrators and geometry optimization are now available:

• Velocity Verlet (NVE) — microcanonical ensemble
• Langevin dynamics (NVT) — BAOAB splitting for optimal stability
• Nosé-Hoover Chain (NVT) — deterministic thermostat
• NPT/NPH ensembles — Martyna-Tobias-Klein barostat with dynamic cell fluctuations
• Velocity rescaling — direct temperature control
• FIRE2 optimizer — adaptive timestep geometry optimization with variable cell support

All integrators support both single-system and batched computation modes.

JAX Bindings (#24)

A new nvalchemiops.jax namespace provides JAX JIT-compatible wrappers for neighbor lists, electrostatics (Ewald, PME), DFT-D3 dispersion, splines, and batch utilities. Warp kernels are exposed via warp.jax_experimental.jax_kernel.

Note: Cell list operations that require runtime-dependent array allocation are not yet JIT-compatible. JAX autograd (differentiation) support is not yet implemented.

Damped Shifted Force (DSF) Electrostatics (#21)

A new O(N) electrostatics method is available via nvalchemiops.torch.dsf and nvalchemiops.jax.dsf:

• Full PBC and virial stress tensor support
• CSR and dense neighbor matrix formats
• Charge gradient support via straight-through estimator for MLIP training
• Benchmarks show ~80× speedup over PME at 54k atoms; scales to 195k atoms where Ewald/PME encounter memory limits

Differentiable Virial for Ewald and PME (#20)

Ewald and PME now support analytical stress tensor computation via a new compute_virial parameter. Virial is computed in the forward pass and attached to the autograd tape, enabling stress-based loss functions for MLIP training. Typical overhead: +5–12% for Ewald, +8–27% for PME.

compute_charge_gradients in ewald_summation (#27)

The high-level ewald_summation() now accepts compute_charge_gradients=True, forwarding it to both ewald_real_space() and ewald_reciprocal_space() components. Previously only available via the low-level APIs.

GPU-Side Batch Rebuild Detection and Selective Skip (#38)

Per-system neighbor list rebuild detection now runs entirely on the GPU with no CPU–GPU synchronization:

• batch_neighbor_list_needs_rebuild() and batch_cell_list_needs_rebuild() return per-system boolean flags
• All neighbor list APIs (naive, batch_naive, cell_list, batch_cell_list) accept an optional rebuild_flags tensor to skip non-rebuilding systems at the kernel level
• Available in PyTorch and JAX bindings

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Breaking Changes

... (truncated)

Changelog

Sourced from nvalchemi-toolkit-ops's changelog.

Changelog

0.3.0 - 2026-XX-XX

Breaking Changes

• PyTorch is now an optional dependency: The previous PyTorch-based functionality has been moved to a separate nvalchemiops.torch namespace. See the hosted documentation for a detailed migration guide. Previous imports should still be supported, however will issue deprecation warnings. The old interfaces will be removed in an upcoming release.

Added

• Framework-agnostic Warp kernel layer for all modules (neighbors, electrostatics, dispersion, math/spline) that operates directly on warp.array objects. A best effort to have interfaces that mirror their framework bindings is made, however due to differences in functionalities this may not always be possible.
• Thin PyTorch bindings in nvalchemiops.torch.* that wrap the Warp kernels.
• Deprecation warnings for old import paths to guide migration.
• JAX bindings in nvalchemiops.jax.* that wrap the Warp kernels, providing support for neighbor lists, DFT-D3 dispersion, electrostatics (Coulomb, Ewald, PME), and splines with jax.jit compatibility.
• GPU-accelerated molecular dynamics integrators with single-system and batched modes: Velocity Verlet (NVE), Langevin (NVT), Nosé-Hoover Chain (NVT), NPT, NPH, and Velocity Rescaling
• FIRE (Fast Inertial Relaxation Engine) geometry optimizer with adaptive timestep, variable cell optimization, and cell filtering for constrained optimization
• Lennard-Jones potential with GPU-accelerated energy, force, and virial computation integrated with neighbor lists
• Batch processing utilities (nvalchemiops.batch_utils) with support for both batch_idx (ragged arrays) and atom_ptr (CSR format) including operations: batch_sum, batch_mean, batch_max, batch_min, batch_scale, batch_normalize, batch_gather, batch_scatter
• Cell manipulation utilities including volume calculation, inverse, wrapping, alignment, and transformation
• SHAKE and RATTLE constraint algorithms for bond length constraints and rigid molecules

Commits

• See full diff in compare view

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