gugen 0.4.1

Explainable materials synthesis and process planning
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173

//! gugen (具現): explainable materials synthesis and process planning.
//!
//! This crate turns a target inorganic composition (and optionally a target
//! structure) into candidate precursor sets, balanced reactions, and
//! solid-state process plans — each with its evidence, assumptions, and
//! unresolved conditions kept explicit. It does not predict experimental
//! success. See `docs/scientific_scope.md` for what is and is not in
//! scope, and `CHANGELOG.md` for the user-facing capability list.
//!
//! This implements typed errors, validated numeric types, composition,
//! target specification, the public report schema, provenance, provider
//! trait boundaries, exact
//! reaction balancing, bounded precursor-set search, a solid-state process
//! template, plan scoring/confidence, end-to-end orchestration via
//! `Planner`, an optional `mikiwame` structural-diagnostics adapter, a
//! CLI (`src/bin/gugen.rs`: `plan`, `balance`, `explain`, `validate-target`,
//! `doctor`, `batch`), a validation suite against curated literature
//! fixtures (`tests/`, `docs/benchmark_report.md`), and v0.1 release
//! preparation (license files, docs.rs metadata, a dependency license
//! audit — see `tasks/todo.md`'s Phase 9 section). The `chematic-crystal`
//! adapter remained blocked on that crate's publication through v0.1
//! (Phase 16 below addresses part of this), and two
//! validation findings are documented rather than fixed (see
//! `tasks/todo.md`'s Phase 8 section). **v0.1.0 is published** (crates.io,
//! merged to `main`, tagged `v0.1.0`) — see `tasks/todo.md`'s Phase 9
//! section for the release record. Post-v0.1 development toward v0.2.0
//! (Phase 10-14 — real literature-sourced process conditions, a
//! large-scale blind benchmark, a second route family, a thermodynamic-
//! provider adapter boundary, and a validation-fixture citation repair) is
//! tracked from `tasks/todo.md`'s Phase 10 section onward, not `AGENTS.md`
//! §26 (which only defines the original 9 phases). **v0.2.0 is published**
//! (crates.io, tagged `v0.2.0`). Work toward v0.3.0 has begun with Phase
//! 15A (`route_suitability` module): a report-level evidence model for
//! whether a route family suits a target (`Supports`/`Contradicts`/
//! `Unknown` findings, never an aggregated score). Phase 15B added
//! `derive_recommendation`, a pure function deriving a discrete
//! `RouteRecommendation` from that evidence, and wired only its
//! `NotRecommended` state into `Planner::plan`: a plan with strong,
//! uncontested contradicting evidence is moved from `plans` into the new
//! `SynthesisPlanningReport.not_recommended` (kept, with its findings, not
//! dropped), and a target where every generated plan is excluded this way
//! abstains explicitly via `unresolved` rather than returning an empty
//! success. No numeric score is affected by either phase. Phase 16 added
//! an optional `chematic_crystal` feature: `to_mikiwame_structure`
//! converts a caller-supplied `chematic_crystal::PeriodicStructure` (now
//! published, 0.15.0) into a `mikiwame::OwnedStructure`, closing the
//! specific conversion gap the mikiwame adapter had named since Phase 6.
//! Still not auto-wired into `Planner::plan` -- `TargetSpecification` has
//! no geometry field, so a caller still applies the result themselves.
//! Phase 17 audited how much literature evidence for route suitability
//! actually exists in a real synthesis corpus, and evaluated
//! `derive_recommendation` against a hand-verified holdout record --
//! explicitly not a route-family prediction-accuracy benchmark (see
//! `docs/route_suitability_corpus_audit.md`); no production code changed.
//! Phases 15A/15B/16/17 together are v0.3.0's planned development work.
//! **v0.3.0 is published** (crates.io, tagged `v0.3.0`). Post-v0.3.0
//! development toward v0.4.0 added finite-temperature Gibbs-energy
//! estimation for gas-free solid systems (Phase 19P/19P.1), deliberately
//! not connected to ranking (`thermodynamic_support` stays `None`); a
//! bulk literature-corpus snapshot loader and exact-match observation
//! provider (Phase 20B); cross-DOI field comparison across independent
//! sources for that corpus (Phase 20C); a manual extraction-accuracy
//! audit against original source papers (Phase 20D); and Integration,
//! which surfaces that cross-DOI evidence on
//! `SynthesisPlan.literature_evidence` for reference-only display --
//! never auto-filling `ProcessStep` conditions and never affecting
//! `score`/`confidence`/ranking. Together these are v0.4.0's planned
//! development work: gas-free solid finite-temperature thermodynamic
//! primitives, a bulk literature observation snapshot API, cross-DOI
//! agreement/conflict classification, and reference-only literature
//! evidence in `Planner` -- an evidence-infrastructure release, not a
//! ranking-accuracy or synthesis-success-prediction claim.
//! **v0.4.0 is published** (crates.io, tagged `v0.4.0`). See
//! `CHANGELOG.md` for the user-facing summary.

#![forbid(unsafe_code)]

mod balance;
#[cfg(feature = "chematic_crystal")]
mod chematic_crystal_adapter;
mod composition;
mod config;
mod error;
mod evidence;
mod frac;
mod literature_conditions;
mod literature_evidence;
#[cfg(feature = "literature_corpus")]
mod literature_observation_conflicts;
#[cfg(feature = "literature_corpus")]
mod literature_observations;
#[cfg(feature = "materials_project")]
mod materials_project_adapter;
#[cfg(feature = "mikiwame")]
mod mikiwame_adapter;
mod planner;
mod precursor;
mod process;
mod provenance;
mod provider;
mod reaction;
mod rejection;
mod report;
mod route_suitability;
mod score;
mod target;
mod thermodynamics;

pub use balance::{balance, curated_byproducts};
#[cfg(feature = "chematic_crystal")]
pub use chematic_crystal_adapter::to_mikiwame_structure;
pub use composition::{Composition, ELEMENT_SYMBOLS, Element};
pub use config::{PlanningConfig, SearchBudget};
pub use error::{GugenError, ProviderError, Result};
pub use evidence::{EvidenceKind, EvidenceScope, EvidenceStrength, PlanningEvidence};
pub use literature_conditions::{CuratedConditionRecord, InMemoryLiteratureConditionProvider};
pub use literature_evidence::{
    CrossDoiFieldStatus, LiteratureRouteEvidence, RouteObservationAssessment, SourcedValue,
    StepGroupAssessment, StepGroupKey, literature_evidence_limitations,
};
#[cfg(feature = "literature_corpus")]
pub use literature_observation_conflicts::LiteratureObservationCorpusProvider;
#[cfg(feature = "literature_corpus")]
pub use literature_observations::{
    CORPUS_SNAPSHOT_SCHEMA_VERSION, CorpusHeatingObservation, CorpusManifest,
    LiteratureObservationCorpus, LoadMode, LoadReport, RejectedObservation,
};
#[cfg(feature = "materials_project")]
pub use materials_project_adapter::MaterialsProjectSnapshotProvider;
#[cfg(feature = "mikiwame")]
pub use mikiwame_adapter::{StructuralDiagnosticEffects, structural_effects};
pub use planner::Planner;
pub use precursor::{
    AcceptedPrecursorSet, AvailabilityMetadata, InMemoryPrecursorCatalog, PrecursorCandidate,
    PrecursorId, PrecursorSearchOutcome, PrecursorSelection, search_precursor_sets,
};
pub use process::{
    Atmosphere, CharacterizationMethod, ConditionConflict, ConditionPrecedent, CoolingMode,
    DurationRange, FormingMethod, GrindingMethod, HeatingPurpose, InertGas, MaterialAmount,
    MixingMethod, PlannedStep, PressureRange, ProcessPrecedent, ProcessStep, ProcessTemplateResult,
    RampRateRange, ReducingAgent, RouteFamily, StepRequirement, TemperatureRange,
    applicable_route_family_templates, conventional_solid_state_template, mechanochemical_template,
};
pub use provenance::PlanningProvenance;
pub use provider::{
    LiteratureEvidenceProvider, PrecursorCatalog, ProcessEvidenceProvider,
    RouteSuitabilityProvider, ThermodynamicProvider,
};
pub use reaction::{
    BalancedReaction, CompetingPhase, ReactionEnergy, ReactionSpecies, ThermodynamicConditions,
};
pub use rejection::{RejectedCandidate, RejectionCode};
pub use report::{
    ApplicabilityAssessment, ApplicabilityLevel, NotRecommendedPlan, PlanId, PlanningWarning,
    SCHEMA_VERSION, SynthesisPlan, SynthesisPlanningReport, TargetSummary, UnresolvedRequirement,
    WarningSeverity,
};
pub use route_suitability::{
    CuratedSuitabilityRecord, InMemoryRouteSuitabilityProvider, RouteRecommendation,
    RouteSuitabilityAssessment, SuitabilityFinding, SuitabilityVerdict, derive_recommendation,
};
pub use score::{
    ConfidenceAssessment, PlanAssessment, PlanScoreBreakdown, PlanningAssumption, RankingWeights,
    Score01, ranking_weights_digest, score_plan,
};
pub use target::{
    PhaseRequirement, PlanningConstraints, TargetMaterialView, TargetSpecification, TargetStructure,
};
pub use thermodynamics::{
    DecompositionComparison, Kelvin, SolidThermodynamicEntry, ThermodynamicDatasetIdentity,
    ThermodynamicSelectivityAssessment, balanced_reaction_delta_ev_per_atom,
    decomposition_margin_ev_per_atom, reduced_mass_amu, relative_solid_gibbs_ev_per_atom,
};