Merge pull request #8 from Ladme/v0.10

Version 0.10

Author: Ladme

.gitignore

@@ -1,5 +1,6 @@
 /target
 /Cargo.lock
+/.vscode
 
 analyzer.rs
 old.rs

.vscode/settings.json

@@ -1,45 +1,62 @@
 [package]
 name = "groan_rs"
 description = "Gromacs Analysis Library for Rust"
-version = "0.9.0"
+version = "0.10.0"
 license = "MIT"
 edition = "2021"
 authors = ["Ladislav Bartos"]
 repository = "https://github.com/Ladme/groan_rs"
 keywords = ["gromacs", "molecular-dynamics"]
 categories = ["command-line-utilities", "science"]
 build = "build.rs"
-exclude = ["test_files", ".vscode", "book", "validation"]
+exclude = [
+    "test_files",
+    ".vscode",
+    "book",
+    "comparison",
+    "run_check.sh",
+    "run_check_tests.sh",
+    "run_doc_tests.sh",
+    "run_tests.sh",
+]
 
 [dependencies]
-colored = "2.1"
+colored = "3.0.0"
 float-cmp = "0.10.0"
-indexmap = { version = "2.7", features = ["serde"] }
+indexmap = { version = "2.8.0", features = ["serde"] }
 regex = "1.11.1"
-thiserror = "2.0.4"
-serde = { version = "1.0.215", features = ["derive"] }
+thiserror = "2.0.12"
+serde = { version = "1.0.218", features = ["derive"] }
 serde_yaml = "0.9"
 fancy-regex = "0.14.0"
 nalgebra = "0.33.2"
-minitpr = "0.2.2"
+minitpr = "0.2.3"
 ndarray = "0.16.1"
 hashbrown = "0.15.2"
-getset = "0.1.3"
+getset = "0.1.5"
 parking_lot = { version = "0.12.3", optional = true }
+molly = { version = "0.3.3", optional = true }
+chemfiles = { version = "0.10.41", optional = true }
+itertools = "0.14.0"
+dyn-clone = "1.0.19"
 
 [dev-dependencies]
 file_diff = "1.0.0"
-tempfile = "3.14.0"
-rand = "0.8.5"
+tempfile = "3.19.0"
+rand = "0.9.0"
 criterion = "0.5.1"
 paste = "1.0.15"
 
 [build-dependencies]
-cc = { version = "1.2.1", features = ["parallel"] }
+cc = { version = "1.2.16", features = ["parallel"] }
 
 [features]
+default = ["molly"]
+molly = ["dep:molly"]
+chemfiles = ["dep:chemfiles"]
 serde = ["ndarray/serde", "hashbrown/serde"]
-parallel = ["parking_lot"]
+parallel = ["dep:parking_lot"]
+no-xdrfile = []
 
 [[bench]]
 name = "main"

Cargo.toml

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 Ladislav Bartos
+Copyright (c) 2023-2025 Ladislav Bartos
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

LICENSE

@@ -57,12 +57,24 @@ fn benchmark(c: &mut Criterion) {
         })
     });
 
+    c.bench_function("System::group_estimate_center (Protein)", |b| {
+        b.iter(|| {
+            std::hint::black_box(system.group_estimate_center("Protein").unwrap());
+        })
+    });
+
     c.bench_function("System::group_get_center (Protein)", |b| {
         b.iter(|| {
             std::hint::black_box(system.group_get_center("Protein").unwrap());
         })
     });
 
+    c.bench_function("System::group_estimate_center (Membrane)", |b| {
+        b.iter(|| {
+            std::hint::black_box(system.group_estimate_center("Membrane").unwrap());
+        })
+    });
+
     c.bench_function("System::group_get_center (Membrane)", |b| {
         b.iter(|| {
             std::hint::black_box(system.group_get_center("Membrane").unwrap());

benches/main.rs

@@ -1,26 +1,33 @@
+// Released under MIT License.
+// Copyright (c) 2023-2025 Ladislav Bartos
+
 extern crate cc;
 
 fn main() {
-    // compile the xdrfile library
-    let source_files = vec![
-        "external/xdrfile/xdrfile.c",
-        "external/xdrfile/xdrfile_xtc.c",
-        "external/xdrfile/xdrfile_trr.c",
-        "external/xdrfile/xdrfile_jump.c",
-    ];
-    cc::Build::new()
-        .files(source_files)
-        .include("external/xdrfile")
-        .warnings(false)
-        .flag("-O3")
-        .compile("libxdrfile.a");
+    if std::env::var("CARGO_FEATURE_NO_XDRFILE").is_ok() {
+        // do nothing if `no-xdrfile` feature is enabled
+    } else {
+        // compile the xdrfile library
+        let source_files = vec![
+            "external/xdrfile/xdrfile.c",
+            "external/xdrfile/xdrfile_xtc.c",
+            "external/xdrfile/xdrfile_trr.c",
+            "external/xdrfile/xdrfile_jump.c",
+        ];
+        cc::Build::new()
+            .files(source_files)
+            .include("external/xdrfile")
+            .warnings(false)
+            .flag("-O3")
+            .compile("libxdrfile.a");
 
-    println!("cargo:rerun-if-changed=external/xdrfile/xdrfile.c");
-    println!("cargo:rerun-if-changed=external/xdrfile/xdrfile.h");
-    println!("cargo:rerun-if-changed=external/xdrfile/xdrfile_xtc.c");
-    println!("cargo:rerun-if-changed=external/xdrfile/xdrfile_xtc.h");
-    println!("cargo:rerun-if-changed=external/xdrfile/xdrfile_trr.c");
-    println!("cargo:rerun-if-changed=external/xdrfile/xdrfile_trr.h");
-    println!("cargo:rerun-if-changed=external/xdrfile/xdrfile_jump.c");
-    println!("cargo:rerun-if-changed=external/xdrfile/xdrfile_jump.h");
+        println!("cargo:rerun-if-changed=external/xdrfile/xdrfile.c");
+        println!("cargo:rerun-if-changed=external/xdrfile/xdrfile.h");
+        println!("cargo:rerun-if-changed=external/xdrfile/xdrfile_xtc.c");
+        println!("cargo:rerun-if-changed=external/xdrfile/xdrfile_xtc.h");
+        println!("cargo:rerun-if-changed=external/xdrfile/xdrfile_trr.c");
+        println!("cargo:rerun-if-changed=external/xdrfile/xdrfile_trr.h");
+        println!("cargo:rerun-if-changed=external/xdrfile/xdrfile_jump.c");
+        println!("cargo:rerun-if-changed=external/xdrfile/xdrfile_jump.h");
+    }
 }

build.rs

@@ -1,6 +1,58 @@
 
 ## Changelog for the `groan_rs` library
 
+### Version 0.10.0
+
+#### New XTC Parser
+- Now using [`molly`](https://crates.io/crates/molly) for faster reading of XTC files. Requires the `molly` feature to be active, otherwise the standard `xdrfile` library is used. With `molly` iterating through XTC files is ~50% faster compared to `xdrfile`.
+- Implemented an efficient "partial-frame" XTC reader using `molly`. It attempts to only read atoms of a specified group while ignoring the rest of the atoms. See `GroupXtcReader` and `System::group_xtc_iter` for more information.
+- `GroupXtcReader` implements a new trait `TrajGroupReadOpen`.
+
+#### Integration with the `chemfiles` Library
+- All trajectory file formats supported by `chemfiles` can be now read using `System::traj_iter<ChemfilesReader>`. However, only XTC, TRR, TNG, DCD, Amber NetCDF, and LAMMPSTRJ are independently tested by `groan_rs`. Be careful when working with other file formats since these may not work properly.
+- To enable integration with `chemfiles`, you have to enable the `chemfiles` feature. If you do this, you need to have `cmake` version LOWER than 4.0.
+
+#### More Precise Center of Geometry/Mass Calculations
+- **IMPORTANT Breaking changes:**
+  - Implemented the Refined Bai-Breen algorithm similar to the pseudo-center of mass recentering algorithm described in https://arxiv.org/abs/2501.14578.
+  - Methods `AtomIteratorWithBox::get_center` and `AtomIteratorWithBox::get_com` using the original Bai-Breen algorithm have been RENAMED to `AtomIteratorWithBox::estimate_center` and `AtomIteratorWithBox::estimate_com`, respectively.
+  - Similarly, `System::group_get_center` and `System::group_get_com` have been renamed to `System::group_estimate_center` and `System::group_estimate_com`.
+  - New functions called `AtomIteratorWithBox::get_center`, `AtomIteratorWithBox::get_com`, `System::group_get_center`, `System::group_get_com` use the **Refined Bai-Breen algorithm** which consists of 1) calculating the pseudo-center of geometry of the selected atoms, 2) making the group whole in the simulation box, 3) naive calculation of center of geometry or mass in the simulation box.
+  - The refined Bai-Breen algorithm is much more precise than the original Bai-Breen algorithm but only works for groups that are smaller than half the simulation box. It is also ~50% slower than the original Bai-Breen algorithm.
+  - All internal `groan_rs` methods now use the Refined Bai-Breen algorithm, with the exception of `System::atoms_center` and `System::atoms_center_mass` which continue to use the original Bai-Breen algorithm but are recommended to only be used for visual centering.
+
+#### CellGrid
+- Implemented a `CellGrid` (also known as cell lists) structure for efficient pairwise distance calculations within a cutoff.
+- New atom iterator, `UnorderedAtomIterator`, has been implemented.
+- `System::guess_bonds` has been reimplemented using a `CellGrid` making it **much** more efficient, especially for large systems.
+- **Breaking change:** `System::guess_bonds_parallel` has been removed. (But the new `System::guess_bonds` is now much faster than `System::guess_bonds_parallel` has been.)
+
+#### Hydrogen Bond Analysis
+- Implemented a way to identify hydrogen bonds (`HBondAnalysis`) in a trajectory. The analysis can be performed with any trajectory reader (`HBondTrajRead::hbonds_analyze`).
+
+#### Changes to Trajectory Iteration
+- **Breaking change:** `TrajReadOpen` trait has been renamed to `TrajFullReadOpen`. The original `TrajReadOpen` trait now requires implementing the `initialize` method which can be used to construct either `TrajFullReadOpen` structure 
+
+#### Changes to `System::traj_iter_map_reduce` (as is tradition)
+- **Breaking changes:** 
+  - The `Data` structure in `System::traj_iter_map_reduce` no longer needs to implement `Add`. Instead, it needs to implement `ParallelTrajData` which requires the user to specify how the data structures should be reduced (merged). `ParallelTrajData` also allows the user to provide a custom `initialize` function which accepts thread ID and is automatically called after spawning a thread. This allows the user to implement thread-specific behavior or to properly sort the final results.
+  - `System::traj_iter_map_reduce` can be now provided a group name in case a "partial-frame" iteration should be performed. In such case, the provided `Reader` structure must be `GroupXtcReader`.
+  - The `Reader` structure in `System::traj_iter_map_reduce` still needs to implement `TrajReadOpen` but it's the new trait (see 'Changes to Trajectory Iteration`).
+  - Made error propagation better. If a single thread encounters an error, all other threads will abort within 10 trajectory frames.
+
+#### Expansion of Utilities for Ignoring PBC
+- Introduced `NaiveShape` trait for geometry filtering ignoring PBC and implemented this trait for `Sphere`, `Rectangular`, and `Cylinder`.
+- Implemented `ImmutableAtomIterable::filter_geometry_naive` and `MutableAtomIterable::filter_geometry_naive` for geometry filtering of atoms from iterators ignoring PBC and box dimensions.
+
+#### Other Changes
+- Introduced `Atom::reset_bonded` and `System::clear_bonds` for simpler removal of bonding information.
+- Sodium atoms should be less often misclassified as sulfur when guessing elements.
+- Reworked how groups are stored inside a system. Introduced a new `Groups` structure for storing groups.
+- **Bug fix:** Fixed undefined behavior in xdrfile jumping which lead to TRR files being read incorrectly when using clang.
+- **Bug fix:** Fixed incorrect parsing of some TPR files generated with Gromacs 2025.
+
+***
+
 ### Version 0.9.0
 
 #### Atom Index