SQQ

SQQ: Python Joint Toolkit for Water-Shell Topology Analysis.

Current release: 0.3.5

SQQ provides the complete SQQ-Py water-shell topology workflow plus the focused SQQ-CPP cage engine. Modes 00 and py use SQQ-Py; modes 99 and cpp use C++17 for graph, internal ring, cage, occupancy, and F3/F4 analysis. Algorithms are documented in docs/design.md and release notes in docs/update.md.

Acknowledgements

Names are listed alphabetically by family name. The order does not indicate relative contribution.

• Liwei Cheng - Wuhan Institute of Technology
• Bin Fang - Hainan University
• Jihui Jia - China University of Petroleum (Beijing)
• Wuquan Li - Beijing Huairou Laboratory
• Bo Liao - China University of Petroleum (East China)
• Yingxu Lu - Wuhan Institute of Technology
• Fengyi Mi - Southwest University of Science and Technology
• Zhengcai Zhang - Laoshan Laboratory

Changed in 0.3.5

• Package and native-core versions are synchronized at 0.3.5, released Jul 23, 2026.
• Mode 50 is replaced by py without an alias, and py is the default. The supported presets are 00, py, 99, and cpp.
• Modes py and cpp default to one worker; modes 00 and 99 retain the 100% automatic-core policy with one physical core reserved. Explicit -w overrides the preset.
• No mode emits ordinary, classified, or cluster GRO files by default. Modes 00 and py default to info,sqq-cage-gro,sqq-render,summary-xlsx; modes 99 and cpp default to info,sqq-cage-gro,sqq-render,summary-csv.
• Generated VMD scripts use explicit cage/guest commands such as sqq show cage 512, sqq show guest 512, sqq color cage 512 green, and sqq color guest 512 yellow. Sourcing the script prints concise help and starts with sqq show cage all.
• sqq-cage.gro now retains guest-to-cage memberships, including multi-cage assignments and every atom of a multi-atom guest. Cage networks use DynamicBonds; guests use CPK.
• Mandatory runtime metadata is written atomically to config.yaml. Detailed config worksheet/CSV tables are removed, while the summary dashboard keeps a compact Configuration block.

Install

Install the released package from PyPI:

pip install sqq

Upgrade an existing installation:

pip install -U sqq

For local development from a source checkout:

pip install -e .

Building from source compiles the native extension and requires a C++17 compiler, CMake 3.20 or newer, Python development headers, and a platform build tool. Normal releases are intended to install a prebuilt wheel and do not compile C++ on the user's machine.

Then use:

sqq -h
sqq --version
sqq init -o config.yaml
sqq analyze -i ./gro -c config.yaml -o ./result_sqq

Root help prints the SQQ version and release date immediately before the usage line. Use sqq -v or sqq --version for the version line alone.

During source-tree development without installation:

python -m sqq analyze -i ./gro -c config.yaml -o ./result_sqq

Quick Start

Single GRO file:

sqq analyze -i test1.gro -o ./result_sqq

Directory of GRO files:

sqq analyze -i ./gro --pattern "*.gro" -o ./result_sqq

For multiple GRO files, SQQ groups compatible frames automatically. Files with one topology share the requested output root; heterogeneous inputs are separated into result_A, result_B, and so on in first-occurrence order. The grouping affects aggregation and paths only, not per-frame analysis.

Glob pattern:

sqq analyze -i "./gro/*.gro" -o ./result_sqq

XTC/TRR trajectory with a topology file:

sqq analyze -i traj.xtc --top topol.gro -c config.yaml -o ./result_sqq

LAMMPS dump or DCD with a DATA topology; standard water/methane types are inferred automatically:

sqq analyze -i traj.lammpstrj -t system.data -o ./result_sqq

Input Units and Boxes

GRO and MDAnalysis trajectory coordinates are interpreted in nm. GRO accepts exactly one frame per file and rejects truncated atom blocks, missing or malformed box lines, extra non-empty records, and non-finite coordinates. Trajectory frames also require finite coordinates. XYZ coordinates are multiplied by input.xyz_scale / --xyz-scale; the default 0.1 assumes angstrom input, while 1.0 keeps nm values. SQQ accepts exactly one declared XYZ frame per file and rejects truncated, extra, malformed, or non-finite atom records. XYZ has no periodic box unless converted through another format.

GRO atom counts and the mandatory box line are validated. A three-value positive box is orthorhombic; an all-zero box is treated as non-periodic. Nine-value GRO boxes with nonzero tilt terms and trajectory frames with non-90-degree angles are rejected because triclinic minimum-image calculations are not implemented. GRO molecules are formed from contiguous residue blocks in source order, preventing wrapped or repeated residue IDs from merging distinct molecules. LAMMPS normally uses DATA molecule IDs; automatic inference can rebuild them from unambiguous Bonds components, and dump atom rows may be interleaved.

LAMMPS trajectories require -t system.data (equivalent to --top / --topology). A non-empty input.lammps.type_map explicitly maps every numeric atom type to resname/atomname or ignore and always takes priority. If the map is absent or empty, SQQ uses DATA masses, type comments, and Bonds to infer only unambiguous standard water (1 O + 2 H, two O-H bonds), all-atom methane (1 C + 4 H, four C-H bonds), and labeled single-site methane mappings. If molecule IDs do not define valid molecules but Bonds do, SQQ rebuilds deterministic molecule IDs and reports that decision. Ambiguous masses, inconsistent reuse of one numeric type, unsupported molecular topology, or insufficient topology evidence fail with a request for an explicit map. The resolved mapping is recorded in config.yaml, per-frame info, and main-summary configuration. This normalization is shared by SQQ-Py and SQQ-CPP. Supported inputs are LAMMPS DATA with full, molecular, bond, or angle atom style, fully periodic pp pp pp orthorhombic dump boxes, and LAMMPS DCD. Tilted boxes, nonperiodic dump boundaries, units lj, duplicate atom IDs, ambiguous molecule reconstruction, and topology/trajectory ID mismatches fail before analysis. input.trajectory_stride applies to XTC, TRR, LAMMPS dump, and LAMMPS DCD.

Analysis Modes

-m / --mode selects one of four presets; the default is py:

sqq analyze -i ./gro -m 00 -o ./result_rigorous
sqq analyze -i ./gro -m py -o ./result_standard
sqq analyze -i ./gro -m 99 -o ./result_cpp_hbond
sqq analyze -i ./gro -m cpp -o ./result_cpp_auto

For SQQ-Py, --find-cluster overrides YAML, which overrides the mode preset. Mode 00 enables cluster search, while mode py leaves it off. Search results enter selected info/main-summary outputs, but no mode selects cluster-gro by default; request it explicitly when split cluster structures are required. Modes 99 and cpp reject --find-cluster on.

Modes py and cpp default to one worker. Modes 00 and 99 use 100% of detected physical cores, reserve one physical core, and are capped by independent files or selected trajectory frames. -w / --worker overrides the preset: integer text is a worker count, while 0.5, 1.0, 50%, and 100% are physical-core fractions. Process parallelism supports independent GRO/XYZ files and indexed XTC/TRR/LAMMPS trajectories. At most 3 * workers tasks are submitted at once.

The default chordless/bounded path preserves the established scientific definitions while accelerating neighbor generation, incremental chord pruning, L1 forward checking, cached layer growth, integer-mask subset ownership, and cage target/edge state pruning. Cage DFS also applies exact remaining-edge incidence and parity conditions before expansion. MDAnalysis supplies orthorhombic cutoff candidates when available, but SQQ still rechecks every distance and hydrogen-bond angle with its established float64 logic. F3 and graph-mode Q_l share one graph-vector cache; all Q_l degrees share candidate lists and spherical-angle work. Optional ring.definition: shortest_path applies the Franzblau shortest-path criterion and reuses bounded-BFS distance maps. Optional quasi_cage.search_policy: exact preserves distinct frontiers and enumerates connected L2/L3 subsets; these opt-in modes can change or add results. Candidate and state truncation is reported through frame warnings.

Every cage now passes the same mandatory topology validation in SQQ-Py and SQQ-CPP: each edge belongs to exactly two faces, V - E + F = 2, the face shell is connected, every vertex link is one cycle, and every shell vertex is trivalent. Optional scientific cage validation adds PBC-aware face-planarity and edge-variation limits, nonzero projected area, positive-volume validation, and volume-centroid cage centers. It remains disabled by default, but disabling it no longer bypasses topology validation. SQQ uses an orthorhombic box representation and rejects non-orthogonal/triclinic input explicitly.

The current release uses the same compact three-row stage model for serial and parallel progress: file preparation (reading, settings, selecting), core topology search (graph, ring, half/quasi, cage, and optional cluster), and post-processing (filtering, order, ice, output). In interactive single-file runs, the active stage is highlighted with bold bright-blue ANSI text. The cluster stage appears only when hydrate-cluster analysis is enabled. Parallel runs also show aggregate stage counts and up to six active files with per-stage and per-file timings.

Native SQQ-CPP Backend

Modes 99 and cpp select the focused native engine. Python owns input normalization, molecule selection, scheduling, annotated GRO/VMD output, Markdown, summary CSV, and optional XLSX; C++17 performs graph construction, internal chordless 4/5/6 rings, cage topology/isomers, occupancy, and F3/F4 while releasing the GIL.

Both accept orthorhombic GROMACS/LAMMPS inputs, compatible graph/pair settings, -s within 4/5/6, cage report/validation settings, f3/f4, process or serial scheduling, and info, gro, cage-gro, sqq-cage-gro, sqq-render, summary-csv, or summary-xlsx. sqq-render implies sqq-cage-gro. gro enables the supported classified cage GRO output, but cpp does not select it by default.

Unsupported requests fail before analysis: public ring output, size 7, shortest-path rings, half/quasi cages, cluster, ice, Q_l/MCG/DHOP, membership/order TSV, legacy per-frame vmd, detail CSV, Python fast closure, thread scheduling, and triclinic boxes. A failed native extension never falls back to Python.

The mode-cpp default layout is:

result/
  sqq-cage.gro
  sqq-render.vmd.tcl
  summary/
    summary.csv
    cage.csv
    cage_occupancy.csv
    cage_isomer.csv
    order_parameter.csv
  config.yaml
  frame_name/
    frame_name_info.md

Neither native mode selects ordinary/classified GRO by default. Modes 99 and cpp write classified cage GRO only when gro or cage-gro is selected explicitly.

Release CI is configured to build and test precompiled wheels for CPython 3.10-3.14 on Windows x86_64, Linux x86_64, macOS x86_64, and macOS arm64, plus a source distribution. A wheel already contains the platform-native extension; end users installing such a wheel do not compile C++. A source install instead invokes the CMake/scikit-build-core build and therefore needs CMake 3.20 or newer and a local C++17 toolchain.

Common Commands

Write a default configuration file:

sqq init -o config.yaml

Search 4/5/6 ring faces and report Type H cages:

sqq analyze -i md.gro -s 4,5,6 --cage-size H -o ./result_sqq_456

Explicitly report every detected cage composition in the selected search scope:

sqq analyze -i md.gro -s 4,5,6 --cage-size all -o ./result_sqq_all_cages

Analyze connected hydrate clusters from all detected cages:

sqq analyze -i md.gro -s 4,5,6 --find-cluster on -o ./result_sqq_cluster

Enable bounded outer quasi-cage layers, or opt into exact connected-subset growth:

sqq analyze -i md.gro --quasi-max-layer 3 -o ./result_sqq_l3
sqq analyze -i md.gro --quasi-max-layer 3 --quasi-search-policy exact -o ./result_sqq_l3_exact

Opt into Franzblau shortest-path rings:

sqq analyze -i md.gro --ring-definition shortest_path -o ./result_sqq_sp_ring

Opt into stricter scientific cage validation:

sqq analyze -i md.gro --cage-scientific-validation on -o ./result_sqq_scientific

Select F3/F4 plus a LAMMPS-style Q_l degree list and neighbors:

sqq analyze -i md.gro --order-parameter f3,f4,q4,q6,q8,q10,q12 --q-neighbor-mode lammps --q-cutoff 0.35 --q-n-neighbor 12

Select all F3/F4 and hydrate-nucleation descriptors:

sqq analyze -i md.gro --order-parameter f3,f4,mcg1,mcg3,dhop35,dhop30 -o ./result_sqq_order

--order-parameter replaces the complete selection rather than adding to the default. Use all for f3,f4,q6,q12,mcg1,mcg3,dhop35,dhop30, or none to skip all order-parameter calculations.

Select the complete output set with one positive option:

sqq analyze -i md.gro --output-type info,cage-gro,summary-xlsx -o ./result_sqq_report
sqq analyze -i md.gro --output-type none -o ./result_sqq_config_only

Default outputs come from the selected mode. Modes 00 and py use info,sqq-cage-gro,sqq-render,summary-xlsx; modes 99 and cpp use info,sqq-cage-gro,sqq-render,summary-csv. No preset includes ordinary, classified, or cluster GRO. config.yaml remains mandatory.

Parallelize independent GRO/XYZ files with spawned processes (the default backend):

sqq analyze -i ./gro --pattern "*.gro" --parallel-backend process -w 4 -o ./result_sqq

The same process backend parallelizes selected frames of one indexed trajectory:

sqq analyze -i traj.xtc --top topol.gro -w 4 -o ./result_sqq

Use --parallel-backend serial for an exact one-process comparison. thread is retained as a compatibility backend, but CPU-bound Python topology search should normally use process.

Important Defaults

mode: "py"

input:
  pattern: "*.gro"
  trajectory_stride: 1
  xyz_scale: 0.1
  lammps:
    units: real
    timestep: 1.0
    atom_style: full
    coordinate_convention: auto
    type_map: {}  # optional override; empty enables strict DATA inference

graph:
  bond_mode: auto
  oo_cutoff_nm: 0.35
  hbond_distance_nm: 0.35
  hbond_angle_deg: 30.0

ring:
  sizes: [4, 5, 6]
  report_sizes: auto
  chordless: true
  definition: chordless

quasi_cage:
  enabled: true
  base_sizes: auto
  side_sizes: auto
  max_layers: 1
  search_policy: bounded

cage:
  enabled: true
  report_types: auto
  max_faces: 20
  search_mode: grow
  seed_mode: ring
  fast_closure: true
  fast_closure_max_states: 20000
  scientific_validation: false
  max_face_planarity_rms_nm: 0.06
  max_face_edge_cv: 0.35
  min_cage_volume_nm3: 1.0e-6
  occupancy_mode: polyhedron

guest:
  resnames: [CH4, CO2, MET, ETH]
  center_atoms:
    CH4: [C]
    CO2: [C]
    MET: [C]
  center_mode: center_atom

hydrate_cluster:
  enabled: false
  min_cage: 2

hydrate_order:
  mcg_guest_resnames: [CH4, MET]
  mcg_guest_cutoff_nm: 0.90
  mcg_water_cutoff_nm: 0.60
  mcg_cone_half_angle_deg: 45.0
  mcg_min_waters: 5
  dhop_neighbor_cutoff_nm: 0.35
  dhop_planar_counts: [11, 12]
  dhop_min_qualified_neighbors: 3

order:
  parameters: [f3, f4]
  q_neighbor_mode: graph
  q_cutoff_nm: 0.35
  q_n_neighbor: null

output:
  types: [info, sqq-cage-gro, sqq-render, summary-xlsx]
  summary_csv_dir: summary
  summary_detail_dir: summary_detail
  cage_isomer_rows: nonzero
  write_empty_files: false
  structure_layout: grouped

parallel:
  backend: process
  workers: auto
  math_threads: 1

Configuration priority:

built-in defaults < mode preset < config.yaml < explicit command-line options

Parallel Execution

parallel.backend: process is the default for two or more independent GRO/XYZ inputs. SQQ uses the spawn start method on every supported platform. Each worker receives run configuration once, reads and writes its own frame, and sends only small stage events plus one summary row to the main process. This avoids the Python GIL limitation of the compatibility thread backend.

Before dispatching two or more GRO files, SQQ reads only their topology records and assigns topology groups in first-occurrence order. The fingerprint contains the atom count and ordered contiguous residue blocks, represented by each block's residue name and ordered atom-name sequence. Titles and time labels, coordinates, velocities, boxes, and numeric atom/residue IDs do not affect grouping. A supplied GRO --top is checked against every input fingerprint; any mismatch fails before analysis and identifies the exact source file.

All accepted groups use one shared worker pool and one global progress index. Each task also carries a group-local frame index and output root, so group summaries and annotated bundles remain correctly ordered without running groups serially. Requested graph.bond_mode: auto remains recorded as auto, but its effective hbond or oo mode is resolved once from a representative frame in each topology group and reused by both SQQ-Py and SQQ-CPP for every frame in that group.

With parallel.workers: auto, modes py and cpp resolve to one worker, while modes 00 and 99 use 100% of detected physical cores before reserving one physical core and applying the file/frame cap. Physical-core detection prefers optional psutil, then platform probes such as Windows CIM, macOS sysctl, or Linux /proc/cpuinfo; if physical cores cannot be detected, SQQ falls back to the CPU count visible to the process. --worker / -w accepts either a fraction (50%, 0.5, or 1.0 for 100%) or an explicit positive integer worker count (1 means one worker). Windows ProcessPoolExecutor runs are capped at 61 workers; Linux workstations can use larger explicit values such as -w 100, subject to the reserve-one-core rule, task count, memory, and storage throughput.

One XTC/TRR or supported LAMMPS trajectory with --top is frame-parallel when the process backend resolves to more than one worker. Every worker opens a private MDAnalysis Universe once and seeks small contiguous batches of selected raw frame indexes; batch size is automatically bounded from 1 to 8, and complete coordinate arrays are not serialized between processes. Parent and worker trajectory readers are explicitly closed. Multiple trajectory files and the compatibility thread backend use the serial trajectory reader.

Process submission uses a bounded rolling queue of at most 3 * workers tasks. This is a queue-depth limit, not a CPU limit: with 100 effective workers SQQ may keep up to 300 tasks submitted while still running as many as 100 workers concurrently. Results are restored to original file/frame order before main-summary writing.

The parent preserves original input order globally and group-local order in every selected group summary and annotated bundle. Output-name collisions are resolved deterministically within each topology group. Process runs set OMP_NUM_THREADS, OPENBLAS_NUM_THREADS, MKL_NUM_THREADS, VECLIB_MAXIMUM_THREADS, NUMEXPR_NUM_THREADS, and BLIS_NUM_THREADS to parallel.math_threads while workers are spawned, then restore the parent environment.

The scheduling and search-cache refinements themselves do not change existing scientific definitions or values. Before the new hydrate descriptors were enabled, they reduced the local 1200ns.gro serial run from about 26.6 s to 18.2 s. A 0.2.3 benchmark that also selected MCG-1 and DHOP35 completed in about 21.6 s on the same host; every overlapping pre-existing analysis column matched the earlier workbook. Performance depends on data, configuration, CPU, memory, and storage.

Search and Report Scope

-s / --size defines the ring-face sizes used during detection and, by default, reporting. With no dedicated report filter, SQQ reports all rings, quasi-cages, and cages found in that search scope. --ring-size and --cage-size can narrow the user-facing output afterward:

# Search 4/5/6, report only ring 5/6 and the Type H cage group
sqq analyze -i md.gro -s 4,5,6 --ring-size 5,6 --cage-size H

For example:

# Report every detected 4/5/6 ring, quasi-cage, and cage composition
sqq analyze -i md.gro -s 4,5,6

# Keep 4/5/6 rings and quasi-cages, but report only structure-I and structure-II cages
sqq analyze -i md.gro -s 4,5,6 --cage-size I,II

Cage report groups expand to scientific cage compositions:

I     -> 5¹², 5¹²6²
II    -> 5¹², 5¹²6⁴
H     -> 5¹², 5¹²6⁸, 4³5⁶6³
HS-I  -> 5¹², 5¹²6², 5¹²6³
TS-I  -> 5¹², 5¹²6², 5¹²6³
I2II  -> 5¹²6³

Repeated cage types contributed by multiple groups are reported once. All detected cages still participate in half-cage, quasi-cage, and free-ring filtering. An explicit --cage-size changes user-facing counts and files, not topology ownership. Cage detection supports 4/5/6 faces; ring and quasi-cage detection also support size 7.

--cage-size accepts the comma-separated groups I, II, H, HS-I, TS-I, and I2II. The default auto scope follows --size; all explicitly requests the same all-detected behavior. Use auto or all alone rather than combining either keyword with a group.

Cage Fast Closure and Scientific Validation

One frame-local ring topology index stores ring_by_id, ring centers, edge_to_ring_ids, ring adjacency, and the symmetric distance cache. Half/quasi and cage searches reuse this object instead of rebuilding the same incidence and geometry data.

cage.fast_closure: true is the default. Only when generic grow reaches a configured state limit, SQQ uses an indexed half-cage overlap graph to assemble connected combinations of two to four standard half-cage patches. Every candidate must still match one generated face composition and pass the ordinary closed-polyhedron test. Existing grow detections are retained first, so exhaustive grow output and object ids remain unchanged; fast closure only adds a cage when the bounded grow path missed it. --cage-fast-closure off disables this supplement for exact comparison.

Topology validation is always enabled. Every candidate must use each edge exactly twice, satisfy V - E + F = 2, form one edge-connected face shell, have one cyclic face link around every vertex, and have only trivalent shell vertices. These inexpensive checks reject disconnected, pinched, branched, and non-manifold false cages before type/isomer assignment in both engines.

cage.scientific_validation: false is the default. When enabled with --cage-scientific-validation on, a topologically valid cage must additionally satisfy the configured PBC-aware face-planarity RMS and edge-length coefficient-of-variation limits, nonzero projected face area, and positive minimum triangulated volume. Accepted cages then use the volume centroid instead of the mean cage-water position. Enabling it can therefore remove geometrically distorted cages and can change guest occupancy or geometry-resolved hydrate-cluster edges. The mandatory topology checks can reduce cage, isomer, occupancy, and cluster results relative to earlier 0.3.2 builds that accepted non-manifold shells. Raw ring and half/quasi searches remain unchanged; ownership-filtered free-ring and free-patch outputs can increase when a rejected cage no longer consumes them.

Guest occupancy uses the configured center atom when available. The defaults select CH4, CO2, MET, and ETH as guests and map CH4, CO2, and MET to atom name C, so these residues use their carbon atom under the default guest.center_mode: center_atom. Otherwise, guest atoms are PBC-unwrapped around one molecular anchor before calculating the centroid; the same helper is used by MCG. This correction can intentionally change occupancy counts relative to 0.2.6 or early 0.2.7 results for multi-atom guests crossing a periodic boundary.

Hydrate Cluster

--find-cluster on analyzes every detected cage in the selected search scope. Cages become graph nodes and are connected through complete shared ring faces. When several detected cages reference the same face, ring-plane geometry keeps at most one cage on each physical side. --cage-size filters user-facing cage tables and files only; it does not remove cages from cluster connectivity or phase evidence.

The hierarchy follows the HTR+ idea of classifying hydrate type, domains, and boundaries on a cage-connection graph (DOI 10.1088/1361-648X/ad52df). SQQ implements this independently with labelled shared-face fingerprints, strict local seeds, mutually compatible expansion, and exclusive per-frame domains.

--cluster-min-cage N sets the minimum connected-component size; the default is 2. Smaller components are counted as isolated cages.

Within each cluster, SQQ builds labelled first-shell fingerprints from neighboring cage types and shared-face sizes. Strict local sI/sII/sH seeds initialize phase evidence. The sH templates cover 5^12, 4^3 5^6 6^3, and 5^12 6^8 cages; the earlier two-anchor sH composite is retained as supplemental high-confidence evidence. All three phases expand through mutually compatible face-labelled edges when a candidate has at least two accepted phase contacts. Cages claimed exclusively by one phase form deterministic per-frame domains.

After the exclusive sI/sII/sH domains are finalized, SQQ partitions the remaining cluster cages. A cage enters the generic boundary only when it is outside every phase domain and directly shares a complete cage face with at least one domain cage. Boundary search stops at this first external non-phase layer. Domain cages are never relabelled as boundary, and a direct shared-face contact between different phase domains leaves both endpoint cages in their original phases.

The resulting classified_cage_ids, boundary_cage_ids, ambiguous_cage_ids, and unclassified_cage_ids are mutually exclusive and together cover every cage in a reported cluster. Competing phase claims without boundary membership remain ambiguous; all other residual cages are unclassified. There are no sI-boundary, sII-boundary, sH-boundary, transition, or boundary-context categories. Neighboring cages can still share face-water coordinates in structure views, so cage ownership should be verified from cage IDs or detected cage/ring edges rather than coordinate-set overlap.

The default command uses mode py, so cluster search is off unless enabled by mode 00, hydrate_cluster.enabled, or explicit --find-cluster on. Modes 99 and cpp do not support cluster search. Explicit --find-cluster on|off has highest priority. Cluster search does not alter ring, patch, cage, occupancy, order-parameter, or ice results. Classification is per-frame and independent of the cage reporting filter; temporal grain tracking and crystallographic orientation matching are not implemented.

Cluster search populates every selected info and main-summary output. Split category structures are written only when cluster-gro is selected explicitly; no mode includes it by default. The selected main summary output gains its per-frame hydrate_cluster table, while native category structures are written under grouped layout as <frame>/hydrate_cluster/<frame>_cluster_sI.gro, <frame>_cluster_sII.gro, <frame>_cluster_sH.gro, and <frame>_cluster_boundary.gro. Flat layout places the same filenames directly in the frame directory. All same-category domains and clusters are aggregated into one file per frame. An absent category is omitted unless output.write_empty_files: true.

Cluster GRO files contain only complete water molecules belonging to the selected cage IDs; guests and CNT atoms are excluded. Ambiguous, unclassified, and isolated cages are not exported. Every atom keeps the exact wrapped coordinate from the analyzed frame, and every file keeps the original box; categories are never moved or unwrapped independently. Periodic or percolating networks may therefore still show bonds crossing a box face because no single-copy GRO representation can remove every periodic seam.

Cage IDs are mutually exclusive across sI, sII, sH, and boundary, but adjacent category files can contain the same face-water molecules because neighboring cages physically share them. When resolved cluster search is on and info is selected, Frame Information records find_cluster as on and the report adds one compact Hydrate Cluster hierarchy. Domain rows may be sI, sII, or sH; boundary and compact unclassified rows are subdivided by cage type. The compact unclassified count is the deduplicated unresolved set: stored ambiguous and unclassified IDs plus any uncategorized residual cluster cages. Main summary and cluster-detail output preserve the distinct scientific fields. Counts use unique cage IDs, zero-count rows are omitted, multiple clusters appear sequentially, and isolated appears once as the final top-level row without subtype children.

## Hydrate Cluster

| item               | type         | cage_qty |
| ------------------ | ------------ | -------- |
| cluster_00001      | mixed        | 334      |
| ├ domain_00001     | sI           | ├ 66     |
|   ├ 5¹²            |              |   ├ 13   |
|   └ 5¹²6²          |              |   └ 53   |
| ├ domain_00002     | sII          | ├ 194    |
|   ├ 5¹²            |              |   ├ 131  |
|   └ 5¹²6⁴          |              |   └ 63   |
| ├ boundary         | boundary     | ├ 69     |
|   ├ 5¹²            |              |   ├ 24   |
|   └ 5¹²6³          |              |   └ 45   |
| └ unclassified     | unclassified | └ 5      |
|   ├ 5¹²6³          |              |   ├ 2    |
|   └ 4¹5¹⁰6²        |              |   └ 3    |
| isolated           | isolated     | 5        |

The compact table does not include exact IDs, seeds, confidence values, water/guest membership, or domain adjacency. Add cluster-detail to --output-type for summary_detail/hydrate_domain.csv and one-row-per-cluster summary_detail/hydrate_cluster_detail.csv. Explicit cluster-detail or cluster-gro selection requires cluster search. Turning search off writes neither cluster-detail nor cluster-gro and removes stale generated cluster GRO files. Public motif output is not generated.

Hydrate Nucleation Order Parameters

MCG-1 and DHOP35 were introduced as defaults in 0.2.5. Since 0.2.7, every MCG/DHOP variant is selected explicitly through --order-parameter; the package default is only f3,f4. These descriptors are independent of the optional cage-topology hydrate_cluster classifier: MCG works on selected methane-like guest centers and surrounding waters, while DHOP works on a dedicated O-O neighbor graph. They do not change graph, ring, patch, cage, occupancy, F3/F4/Q_l, hydrate-cluster, or ice results.

MCG follows the mutually coordinated guest definition. Guest pairs within 0.90 nm are connected when at least five waters lie within 0.60 nm of both guests and inside both 45-degree opposing cones. The threshold is at least five, not exactly five. MCG-1 keeps guest nodes with at least one qualifying MCG edge; optional MCG-3 applies a one-pass degree-at-least-three filter to the same qualifying graph. Connected components are measured only through qualifying MCG edges. The default guest residue names are CH4 and MET; change hydrate_order.mcg_guest_resnames for another methane naming convention. If no configured guest type is present, MCG is reported as N/A, not zero.

DHOP builds its own orthorhombic-PBC oxygen graph with hydrate_order.dhop_neighbor_cutoff_nm: 0.35. This 0.35 nm default follows the all-atom TIP4P/Ice implementation used by Li et al.; use 0.325 in YAML when reproducing the original mW-water definition. For each central O-O bond, SQQ counts neighboring plane-normal pairs within 35 degrees (or 30 degrees for DHOP30), selects waters with counts 11 or 12, requires at least three similarly qualified neighbors, includes their first oxygen shell, and reports the largest connected water cluster. DHOP35 and DHOP30 name the angular thresholds, not the O-O cutoff. No transition-state value such as DHOP35=57 is hard-coded; such values are system- and condition-dependent.

Select any combination with names such as --order-parameter mcg1,mcg3,dhop35,dhop30. Selection is separate from the numerical hydrate_order cutoff settings. All cutoff searches use deterministic cell lists and exact float64 minimum-image rechecks; there are no fixed neighbor-array limits.

References: Barnes et al., MCG (DOI 10.1063/1.4871898); Knott et al., MCG nucleation coordinate (DOI 10.1021/jp507959q); DeFever and Sarupria, DHOP (DOI 10.1063/1.4996132); Li et al., all-atom DHOP nucleation pathway (DOI 10.1073/pnas.2011755117).

Useful Options

Bond Mode

Use -b / --bond-mode to override the graph setting supplied by the selected mode or config.yaml:

sqq analyze -i md.gro -b auto
sqq analyze -i md.gro --bond-mode hbond
sqq analyze -i md.gro -b oo
sqq analyze -i md.gro -b pairs --pairs pairs.txt

Available values are auto, hbond, oo, and pairs. --pairs PAIRS.txt used alone remains shorthand for pairs mode. Combining --pairs with -b auto, -b hbond, or -b oo is rejected. Pairs mode requires either --pairs or graph.pair_file in config.yaml.

Output Selection

--output-type TYPE[,TYPE...] replaces the configured list. Mode py defaults to:

output:
  types: [info, sqq-cage-gro, sqq-render, summary-xlsx]

SQQ-Py accepts the established info/TSV/per-frame GRO/summary/detail types plus sqq-cage-gro and sqq-render. gro expands to ordinary ring/half/quasi/cage/ice GRO categories; sqq-cage-gro is a separate run-level annotated trajectory. sqq-render implies sqq-cage-gro.

SQQ-CPP accepts info, gro, cage-gro, sqq-cage-gro, sqq-render, summary-csv, and summary-xlsx, plus all/none. Neither 99 nor cpp selects gro or cage-gro by default. Cluster search fills selected info/main-summary outputs but does not add unselected output types; explicit cluster-gro or cluster-detail requires search. config.yaml is always written.

Explicit CLI selection has precedence:

--output-type > output.types > engine default

--hydrate-cluster, --cluster-detail, --no-output, --write-order-tsv, and the individual --no-* output switches were removed in 0.2.8. They have no compatibility aliases. Likewise, output.disabled_outputs is rejected rather than migrated; configurations must use output.types.

When an existing output directory is reused, SQQ removes known stale files for output types outside the effective selection while preserving unrelated user files. Main-summary and detail-CSV cleanup is restricted to known SQQ-generated filenames inside the currently configured summary_csv_dir and summary_detail_dir; unknown files are preserved, and changing either setting does not make SQQ scan or clean a formerly configured directory. If no per-frame output type is selected and no unrelated file remains, the empty frame directory is removed.

Output Structure

A single GRO file and trajectory inputs retain their established per-frame layout. For two or more GRO files, topology grouping controls only the aggregation root. If every GRO has one compatible topology, all selected outputs are written directly under the requested result directory:

result/
  config.yaml
  summary.xlsx                 # when summary-xlsx is selected
  summary/                     # when summary-csv is selected
    summary.csv
    cage.csv
    ...
  info/
    frame_001_info.md
    frame_002_info.md
  gro/                         # only when ordinary GRO output is selected
    frame_001/
    frame_002/
  sqq-cage.gro                # when sqq-cage-gro is selected
  sqq-render.vmd.tcl          # when sqq-render is selected

When 2-26 distinct topologies are found, groups are assigned letters by first occurrence and each group gets a complete independent result root. No summary, GRO, or VMD bundle combines incompatible systems:

result/
  config.yaml              # batch manifest and source-to-group mapping
  result_A/
    config.yaml
    summary.xlsx               # and/or summary/
    info/
    gro/                       # when selected
    sqq-cage.gro               # when selected
    sqq-render.vmd.tcl         # when selected
  result_B/
    config.yaml
    summary.xlsx               # and/or summary/
    info/
    gro/                       # when selected
    sqq-cage.gro               # when selected
    sqq-render.vmd.tcl         # when selected

If more than 26 topologies are found, SQQ warns and switches the whole multi-GRO run to information-only output. It still analyzes every readable GRO, but writes only the root config.yaml and result/info/*_info.md; summary XLSX/CSV/detail files, ordinary GRO files, annotated cage GRO, and VMD renderer files are all suppressed. This safety override has precedence over mode defaults and explicit output requests.

For normal multiple-GRO groups, Markdown, membership/order TSV, and legacy per-frame VMD reports are placed under info/; ordinary structure files are placed under gro/<frame>/.

sqq-cage.gro concatenates one complete block per successful frame; atom order and the named contiguous residue-block topology must match, while numeric atom/residue IDs may differ. Coordinates and boxes remain wrapped exactly as analyzed. Annotations begin at column 69 as ; SQQ1 m=... and retain water-to-cage plus guest-to-cage memberships; nonmembers use m=-. A guest assigned to several cages keeps every assignment, and every atom of a multi-atom guest remains available to the renderer.

Keep sqq-render.vmd.tcl and sqq-cage.gro together, then source the script from the VMD Tk Console:

source {path/to/sqq-render.vmd.tcl}

Sourcing prints a concise command list, reports SQQ graph: <effective-mode> once, and starts with sqq show cage all. The graph line is printed again only if the effective mode changes. The help spellings are equivalent:

sqq help
sqq -h
sqq --help

The command grammar is explicit:

sqq show <family> <target> [target ...]
sqq color <family> <target> [target ...] <color>

Supported families are cage, guest, phase, cluster, and domain. Examples:

sqq show cage all
sqq show cage 512
sqq show cage 512 51264
sqq show cage 51262_00053

sqq show guest all
sqq show guest 512
sqq show guest 51262_00053

sqq show phase all
sqq show phase sI boundary
sqq show cluster all
sqq show cluster cluster_00001
sqq show domain all
sqq show domain domain_00001

sqq color cage 512 green
sqq color cage 51262_00053 yellow
sqq color guest 512 yellow
sqq color phase boundary orange
sqq color cluster cluster_00001 cyan
sqq color cage all default

For cage, a target is all, a registered cage type, or an exact frame-local cage ID; generic types such as 4^1-5^10-6^2 also accept 4151062. For guest, the same target identifies guests assigned to all cages, to a cage type, or to one exact cage ID. Phase targets are all, sI, sII, sH, boundary, ambiguous, unclassified, or isolated; cluster/domain targets are all or exact IDs. Multiple targets are accepted within one family. The former inferred forms such as sqq show 512 and sqq color 512 blue are not accepted.

Colors accept a case-insensitive VMD color name, an in-range ColorID, or default. Cage and guest overrides are independent and persist across frame/selection changes without rewriting either file. Cage networks use DynamicBonds with a 3.5 angstrom cutoff; guests use CPK and include the full molecule. When a guest belongs to several selected cage types, the same fixed topology priority used for coincident cage edges decides its display layer, independent of command order and ColorID. A single cage layer uses a 0.125 angstrom cylinder radius (0.250 angstrom diameter); multi-type layers remain bounded from 0.125 to 0.130 angstrom.

The renderer manages representations by VMD's stable representation names, so show, color, and frame changes remove only SQQ-created representations and preserve representations added by the user. Rapid frame notifications are coalesced into one pending redraw. Fully unknown cage, cage-ID, guest-selection, cluster-ID, and domain-ID targets are rejected against the complete loaded trajectory; recognized phase names remain valid even when the current frame has no matching membership. Re-sourcing a generated script resets its selection/color state.

Exact cage, cluster, and domain IDs are assigned independently in each frame. Retaining an ID selection while changing frames therefore selects the same frame-local label, not a tracked physical object. Category selections (phase, cluster, or domain) and recognized phase labels simply report no membership when cluster analysis was not run; an explicit cage/type/cluster/domain target that never occurs anywhere in the loaded trajectory is rejected.

When cage or guest objects are shown, the generated VMD script uses the following stable cage-type colors; guest defaults follow the cage type that selected them. The visible shades follow the active VMD ColorID palette.

Ordinary per-frame GRO files are opt-in through gro or individual types. cluster-gro is separately opt-in and requires cluster search; no mode includes either category by default. With --output-type none, only config.yaml remains.

Without --strict, standalone serial/process/thread read failures become failed summary rows and analysis continues where the reader remains usable. Failed inputs appear in summary.xlsx/failures, <summary_csv_dir>/failures.csv, and <summary_detail_dir>/failures.csv when their respective output types are enabled, and always in the mandatory config.yaml run.failures list. With --strict, SQQ re-raises the error after updating config.yaml to status: failed.

GRO structure folders, filenames, and title lines use portable ASCII structure labels since version 0.2.4, for example 5^126^2 and qc_5r_5^36^2_56566. Markdown and main-summary scientific labels retain their readable superscript notation. This avoids Windows GBK/legacy-reader failures caused by Unicode superscript or subscript characters in generated GRO paths and titles.

Each *_info.md report starts with SQQ version, mode/engine, date/time, source, input format, topology when applicable, trajectory stride, frame/time, requested-to-effective graph mode, effective bond mode, ring sizes, status, and molecule counts. Modes display as 00 (sqq-py), py (sqq-py), 99 (sqq-cpp), or sqq-cpp. LAMMPS reports also record units, timestep, atom style, and type-map source.

When quasi-cage or cage isomers are present, the same report adds description tables:

• Quasi Cage Isomer Description explains each observed layered quasi-cage isomer by base ring and L1/L2/L3 ring sequence.
• Cage Isomer Description explains each observed closed-cage isomer by face composition and 6-ring face adjacency pattern.

Cage Occupancy remains a separate table because it describes guest assignment rather than cage topology. It expands exact guest compositions across dynamic columns in source guest order.

summary-xlsx writes the plotting-oriented summary.xlsx workbook. summary-csv uses the same applicable main-table mapping and writes one UTF-8-SIG file per sheet under summary_csv_dir (default summary/), preserving table names, columns, row order, and values without Excel formatting or tabs. The first summary table is a dashboard: Configuration includes SQQ version, requested/effective Graph mode such as auto -> hbond, normalized Order parameters, Find cluster, and normalized Output types; Analysis Results (min / mean / max) reports per-frame min/mean/max values while Frames total / ok / failed stays a run-level count. Analysis tables such as connection diagnostics, ring, half_cage, compact composition-level quasi_cage, cage, optional hydrate_cluster, order_parameter, and ice keep one input file or trajectory frame per row. The other tables have metadata-specific row units: summary is a dashboard, failures has one failed input/frame per row, and detail_index has one generated detail file per row. Detailed configuration tables are not written; the dashboard retains only its compact Configuration block. Ordinary multi-row and isomer tables are written separately under summary_detail_dir only when summary-detail-csv is selected: optional failures.csv, cage_occupancy.csv, cage_isomer.csv, and quasi_cage_isomer.csv. The separate cluster-detail type writes hydrate_domain.csv and hydrate_cluster_detail.csv. The compact quasi_cage table aggregates exact quasi-cage isomers into composition-level columns such as 5r_5²6³, while the detail quasi_cage_isomer.csv keeps nonzero exact isomer rows with quasi_cage_type, isomer, and count. cage_isomer.csv defaults to observed nonzero isomer rows plus per-frame totals; use --cage-isomer-rows all to restore the full zero-filled matrix. The order_parameter table contains only the selected F3, F4, Q_l, MCG, and DHOP columns; --order-parameter none omits it. Focus mean/count columns are written only when order.focus_waters is non-empty. Output type order-tsv writes only selected per-water F3/F4/Q_l values because MCG/DHOP are frame-level descriptors.

Summary construction records rows, columns, cells, bytes, CSV/XLSX write time, formatting time, and final-save time in config.yaml -> run.summary_write; the terminal prints its total seconds. The mandatory output-root config.yaml records final SQQ version, mode/engine, requested and effective graph modes, requested and resolved workers, normalized output types, input metadata, status/failures, and summary timing. Main CSV, XLSX, detail CSV, and config.yaml are written to same-directory temporary files and atomically replaced on success or failure. XLSX sheets above 200,000 cells or 128 columns keep header styling, filter, freeze pane, and fixed column widths but skip costly body-cell formatting; scientific values and table schemas are unchanged.

The hydrate_cluster main-summary table reports the mutually exclusive classified_cage_count, boundary_cage_count, ambiguous_cage_count, and unclassified_cage_count. Optional cluster-detail CSV records add the corresponding cage-id groups and boundary_composition; hydrate-domain CSV records expose only external boundary contacts through external_boundary_contact_count and external_boundary_contact_ids.

Output ownership is:

cage > quasi_cage > half_cage > ring

SQQ-Py cage files include cage waters, CNT center pseudoatoms, and assigned guests. SQQ-CPP cage files omit the synthetic CNT center pseudoatom. Exact guest-composition files are generated from the guest names present in the frame, such as CH4, CH4x2, or CH4+CO2.

See docs/design.md for algorithm details and docs/update.md for release changes.